I worked around it by using an elisp ‘advice’ snippet another user suggested (http://emacs.stackexchange.com/questions/17112/prevent-org-todo-pop-up-window-from-displaying-in-new-frame-dedicated-window)

Before that I wasted several hours trying to ‘fix’ the problem in various ways. I imagine org is overriding default handling for a good reason, but it is frustrating to have to override said functionality with a code-snippet, which will undoubtedly break at some point while I scratch my head to understand how I can fix it!



From: Nicolas Goaziou
Sent: 13 October 2015 9:52 PM
To: Hassan Dar
Cc: emacs-orgmode@gnu.org
Subject: Re: 'org-switch-to-buffer-other-window' prevents customisation ofpop-up buffers by binding key variables [8.2.10 (release_8.2.10 @ c:/ProgramFiles/emacs/share/emacs/24.5/lisp/org/)]


Hello,

Hassan Dar <h@hassandar.com> writes:

> As seen in the following StackExchange questions:
>
> http://emacs.stackexchange.com/questions/14817/how-to-control-where-the-org-todo-keywords-buffer-displays
>
> http://emacs.stackexchange.com/questions/17112/prevent-org-todo-pop-up-window-from-displaying-in-new-frame-dedicated-window
>
> The org-no-popups macro (which is leveraged by '
> org-switch-to-buffer-other-window' let-binds key variables such as
> "display-buffer-alist" to 'nil'.
>
> This ultimately prevents a user from
> customising pop-ups generated by org in the same way they would with
> other pop-up windows.

I'm not a big fan of Org's opinionated way to handle windows either.
However, couldn't you use `display-buffer-overriding-action' in this
case? It is checked before `display-buffer-alist'.

Regards,

-- 
Nicolas Goaziou