What's going to make the filler compress and get proud (sticking above the level set of the inlay and fret board) is the surrounding wood contacting pinching the filler since the inlay won't move either. With this said I suspect that the issue will lesson in time, five years or so depending on how seasoned the fret board is or was at manufacture.
Prior to that if it's bothersome enough what you're already done with sanding blocks will work as it already has for you. You can scrape things level quickly with a single edge razor if you're careful and learn to use the blade without chattering. Follow up with OOOO steel wool to blend it all in.
I don't see a proper answer for you beyond replacing all the inlays with new ones that have been carefully cut and fit so that no filler is required. That would be a big job and the economics would not be there and you still have the possibility that the fret board material is moving and not seasoned.
It's been my experience on a near daily basis that these issues that result from the use of unseasoned wood moving with the seasonal RH swings is that they diminish and eventually go away. Problem is that sometimes it takes long enough that we are all dead.
. Let's hope that's not the case here I'd rather be writing tunes than decomposing.