Yep, looks like the FGC <token>.getSize and the FGU <token>.getSize API commands behave differently.
I ran some testing using the Soldier NPC from the SWADE GMs guide, and using the BalleMap_outdoor1 map from the SmiteWorks battlemap module.
In FGC <token>.getSize returns the size of the original token - in this case 100x100; which is then used to create the defeated marker.
In FGU <token>.getSize returns the size of the token on the map - 40x40 (80% token scaling on a 50x50 grid).
It makes more sense for the getSize API function to return the actual size on the map rather than the original size of the graphics file.
This size is then used to set the size of the defeated marker - which is a % size, not a physical pixel size. In FGC the example I used is 100 - so the defeated marker is set to 100% of the grid. In FGU this will be 40 (in this example) and so the defeated marker will be set to 40% of the grid.
As the FGC ruleset isn't being updated anymore, a simple fix is to use a defeated marker widget size of 100 in the FGU SWADE ruleset code - at line 75 in manager_tokenmarker.lua, replace the current nSize line with local nSize = 100;
The above details are for the ruleset developer, I'm not expecting users to make this change themselves.
In the meantime, I've attached a hotfix extension that should help with this issue. Copy this file to your FGU app data extensions directory, restart FGU (if it's running) and select "HotFix: SWADE FGU Defeated Marker Size" from the extensions list.