But the terminal window size also increases/decreases
In case of GNOME Terminal, this is the intended behavior.
With docking and split screen, there's an external "force" keeping the window size (as measured in pixels) unchanged. This "force" overrides GNOME Terminal's request on preferred window sizes (to fit entire character cells), so usually you get additional unused space on the right and the bottom.
With "regular" (non docked, non maximized etc.) windows there's no such external "force", so either the window size would still slightly change (in order to always accomodate whole cells, in whichever current font size), or you'd no longer have resize increment geometry hints, you'd end up with continuous resize as done by several other terminal emulators such as
None of these solutions is perfect, each has their pros and cons. GNOME Terminal developers decided to go for maintaining the window size as measured in character cells, that is, a zoom option doesn't effect the app running inside (unless some "external force" forces a different size).