Hi,
There was a bug report about message window sizing issues that seems to be caused by the Scope plugin:
https://sourceforge.net/p/geany/bugs/988/
I'm not sure how to "move" the ticket to the Geany-Plugins bug tracker so I'm just sending it here.
If I recall correctly from writing MultiTerm, there's a bug in VTE library where it doesn't size itself properly (maybe something related to using width in characters instead of pixels) and it goes super-huge by default.
For MultiTerm, I remember I had to perform an explicit gtk_widget_set_size_request(wid, N, N) where N was any arbitrary size smaller than expected (I think I chose 100 or 10 or something). Also, I'm not positive, but the VTE widget might also need to be placed in a GtkFrame or similar, and then into an GtkHBox with a GtkVScrollbar (using the VTE's adjustment) next to the VTE into the GtkHBox. I probably just copied how Geany did it, I don't remember for sure, but it works anyway. I could be completely wrong on the cause of the bug, I just wanted to mention since I remember fighting VTE for same issue.
Cheers, Matthew Brush