It's difficult to find a problem with an install without having a clean starting point for comparison. You have to compare your Mac Pro, taking a base point from your MBP don't make much sense since it's a very different Mac.My entry level MBP has a similar sequential read speed as my MP 6,1, which is about 1,350 MB/s. Its write speed is actually much worse at only 450MB/s. However, when starting Anaconda Navigator app, this MBP takes 10 seconds while MP 6,1 takes 21 seconds.
I am wondering if I need to tune/clean up my Mac Pro? Or if it can be done at all?
Make a clone of your Mac Pro disk, fully erase your SSD removing the containers then the partition/etc, then do a clean install and check if you have better opening times.