A little different solution that takes advantage of the fact that adding a
newline preserves the clock in the narrowed buffer. Maybe the right thing
to do is to widen/re-narrow buffer to include the clock within org-clock-in
though if it detects it's in an org capture buffer? Here is my working
solution for now with use-package and advice:


(use-package org
  :straight org-plus-contrib
  :init
  (defun my/org-capture-place-entry ()
    "Place the template as a new Org entry."
    (let ((template (org-capture-get :template))
 (reversed? (org-capture-get :prepend))
 (exact-position (org-capture-get :exact-position))
 (insert-here? (org-capture-get :insert-here))
 (level 1))
      (org-capture-verify-tree template)
      (when exact-position (goto-char exact-position))
      (cond
       ;; Force insertion at point.
       ((org-capture-get :insert-here) nil)
       ;; Insert as a child of the current entry.
       ((org-capture-get :target-entry-p)
(setq level (org-get-valid-level
    (if (org-at-heading-p) (org-outline-level) 1)
    1))
(if reversed? (outline-next-heading) (org-end-of-subtree t t)))
       ;; Insert as a top-level entry at the beginning of the file.
       (reversed?
(goto-char (point-min))
(unless (org-at-heading-p) (outline-next-heading)))
       ;; Otherwise, insert as a top-level entry at the end of the file.
       (t (goto-char (point-max))))
      (let ((origin (point)))
(unless (bolp) (insert "\n"))
(org-capture-empty-lines-before)
(let ((beg (point)))
 (save-restriction
   (when insert-here? (narrow-to-region beg beg))
   (org-paste-subtree level template 'for-yank))
 (org-capture-position-for-last-stored beg)
 (let ((end (point)))
   (org-capture-empty-lines-after)
   (unless (org-at-heading-p) (outline-next-heading))
   (org-capture-mark-kill-region origin (point))
   ;; CHANGE: insert a newline so clock is included
   (if (org-capture-get :clock-in) (insert "\n"))
   (org-capture-narrow beg end)
   (when (or (search-backward "%?" beg t)
     (search-forward "%?" end t))
     (replace-match "")))))))

  (defun my/org-capture (&optional goto keys)
    "Capture something.
  \\<org-capture-mode-map>
  This will let you select a template from `org-capture-templates', and
  then file the newly captured information.  The text is immediately
  inserted at the target location, and an indirect buffer is shown where
  you can edit it.  Pressing `\\[org-capture-finalize]' brings you back to
the \
  previous
  state of Emacs, so that you can continue your work.

  When called interactively with a `\\[universal-argument]' prefix argument
\
  GOTO, don't
  capture anything, just go to the file/headline where the selected
  template stores its notes.

  With a `\\[universal-argument] \\[universal-argument]' prefix argument,
go to \
  the last note stored.

  When called with a `C-0' (zero) prefix, insert a template at point.

  When called with a `C-1' (one) prefix, force prompting for a date when
  a datetree entry is made.

  ELisp programs can set KEYS to a string associated with a template
  in `org-capture-templates'.  In this case, interactive selection
  will be bypassed.

  If `org-capture-use-agenda-date' is non-nil, capturing from the
  agenda will use the date at point as the default date.  Then, a
  `C-1' prefix will tell the capture process to use the HH:MM time
  of the day at point (if any) or the current HH:MM time."
    (interactive "P")
    (when (and org-capture-use-agenda-date
      (eq major-mode 'org-agenda-mode))
      (setq org-overriding-default-time
   (org-get-cursor-date (equal goto 1))))
    (cond
     ((equal goto '(4)) (org-capture-goto-target))
     ((equal goto '(16)) (org-capture-goto-last-stored))
     (t
      (let* ((orig-buf (current-buffer))
    (annotation (if (and (boundp 'org-capture-link-is-already-stored)
 org-capture-link-is-already-stored)
    (plist-get org-store-link-plist :annotation)
  (ignore-errors (org-store-link nil))))
    (entry (or org-capture-entry (org-capture-select-template keys)))
    initial)
(setq initial (or org-capture-initial
 (and (org-region-active-p)
      (buffer-substring (point) (mark)))))
(when (stringp initial)
 (remove-text-properties 0 (length initial) '(read-only t) initial))
(when (stringp annotation)
 (remove-text-properties 0 (length annotation)
 '(read-only t) annotation))
(cond
((equal entry "C")
 (customize-variable 'org-capture-templates))
((equal entry "q")
 (user-error "Abort"))
(t
 (org-capture-set-plist entry)
 (org-capture-get-template)
 (org-capture-put :original-buffer orig-buf
  :original-file (or (buffer-file-name orig-buf)
     (and (featurep 'dired)
  (car (rassq orig-buf
      dired-buffers))))
  :original-file-nondirectory
  (and (buffer-file-name orig-buf)
(file-name-nondirectory
(buffer-file-name orig-buf)))
  :annotation annotation
  :initial initial
  :return-to-wconf (current-window-configuration)
  :default-time (or org-overriding-default-time
    (org-current-time)))
 (org-capture-set-target-location (and (equal goto 0) 'here))
 (condition-case error
     (org-capture-put :template (org-capture-fill-template))
   ((error quit)
    (if (get-buffer "*Capture*") (kill-buffer "*Capture*"))
    (error "Capture abort: %s" (error-message-string error))))

 (setq org-capture-clock-keep (org-capture-get :clock-keep))
 (condition-case error
     (org-capture-place-template
      (eq (car (org-capture-get :target)) 'function))
   ((error quit)
    (when (and (buffer-base-buffer (current-buffer))
(string-prefix-p "CAPTURE-" (buffer-name)))
      (kill-buffer (current-buffer)))
    (set-window-configuration (org-capture-get :return-to-wconf))
    (error "Capture template `%s': %s"
   (org-capture-get :key)
   (error-message-string error))))
 (when (and (derived-mode-p 'org-mode) (org-capture-get :clock-in))
   (condition-case nil
(progn
 (when (org-clock-is-active)
   (org-capture-put :interrupted-clock
    (copy-marker org-clock-marker)))
 (org-clock-in)

 ;; CHANGE: remove inserted newline now that clock is in narrowed buffer
 (save-excursion (if (org-capture-get :clock-in)
     (progn (goto-char (point-max)) (join-line))))
 (setq-local org-capture-clock-was-started t))
     (error "Could not start the clock in this capture buffer")))
 (when (org-capture-get :immediate-finish)
   (org-capture-finalize))))))))

  (advice-add 'org-capture-place-entry :override
#'my/org-capture-place-entry)
  (advice-add 'org-capture :override #'my/org-capture)
  )