I've dealt with several applications with various sizes. What I've observed is that for applications with an MPR filesize of < 50 MB there is little difference in day-to-day performance. This is also in line with the filesize from which GitHub starts warning users about Git performance, so I would expect this to be a performance consideration that also exists for the Mendix platform.
Some of our larger applications are hosted on private Git servers, so this I cannot say with confidence that the comparison for these larger applications will be relevant to your case. However, with that said, the performance degrades significantly with applications larger than 100 MB, similar to your case.
There might be a relevant setting for you to test though (introduced with 10.12):
Clone Type | Mendix Documentation
You can now specify the clone type for partial clones. Maybe this will help with the performance of checkouts in your situation.
Upgraded several projects from Mx9 to Mx10, none showed this symptom. But the projects were all around 50 to 80 MB.