There are approximately ~1000 bugs reported against MATE Desktop. We are a small team with limited resources, we do the best we can but the fact is “your” bug might not be one we’re actively working on. Placing a decent Bounty on a bug can help motivate developers to prioritise what they’re working on.
As it happens we been looking at over scaled icons from Qt applications in mate-indicator-applet this weekend. It is a very tricky issue to debug, perhaps you could come and help with some bug triage on GitHub?