I use fvwm2 in click-to-type mode and just as a personal preference I
modified the X11 nethack to centre its popups over the main window
rather than over the mouse, so I can leave the mouse away to the side
when not in use.
Others using click-to-type might like this too, so here, as a
suggestion, is a patch which adds an option for this.
cd nethack-3.2.2
patch -p1 <centerpopups.diff
The option is an X resource NetHack*centerPopups and there's a
description of it added to debian/NetHack.ad. By default it's
disabled, so the current behaviour is unchanged.
Also included is a one-line addition to wintext.c to let the keyboard
work on text popups (intro, rip, etc) without the mouse over them,
which is useful if they're not going to be positioned under the mouse.
While doing this I found NetHack*autofocus:true intereferes with
click-to-type. (After the first popup the keyboard works in the main
window only if the mouse is over it.) I added a line to NetHack.ad
about this.