Looks like upgraded buildings use the Scaling Value of the first tier building only...
You could try replacing it when the research is done. Sorta like this...
Event
Unit Finishes an upgrade
Conditions
(Triggering Unit) Equal to (Your tier 1 tower type)
Actions
Unit - Replace (Triggering Unit) with (Your tier 2 tower type)
Or maybe you have to use "(Your tier 2 tower type)" in the conditions too, that'd make sense... I haven't tested it. One of the two should work :X
EDIT: Oh yeah, there's an action called 'Animation - Change Unit Size'. I forgot about that. Just use that then...