The flange they adapted was done pretty badly so it isn't making as even contact as would be ideal. Looks like they tried to use sealant to make up for it and didn't use enough, so it still had gaps.
If it were my circus, I'd use butyl sheet under the boot for more expansion/contraction tolerant waterproofing and take the extra time to do a better job on that flange.
You could go ham with some roof patch and be done with it for a decade and do it better when it needs redoing.