Gnome3 Terminal restores previous window size on focus loss

This is apparently a bug.

https://bugs.launchpad.net/ubuntu/+source/gnome-terminal/+bug/1040885

They mentioned a workaround, select the first tab and resize. Apparently this only happens when the first tab isn't selected.

Usual user settings for a Terminal window sizing based on the rows and columns.
Not a pixel size. So you need change Profile Preferences.

Edit > Profile Preferences > General > Default Size ( columns / rows )

Or to maintain different window sizes for Terminal you can create new profiles for each:

Edit > Profiles > New
Name your new profile and tune it.
Later you can switch them Terminal > Change Profile

Also window sizing templates already exist in menu Terminal

Update:

However, also look this Q/A:
Setting gnome-terminal window size from within ~/.bashrc

it means that ~/.bashrc configuration can override columns/rows size.