That is the right boot for that job. That said, the install is not the most attractive I’ve seen.
If you want to put another boot on top of that, look for “ag panel roof boot” on Google. There are some larger boots that could sit on top of that thing.
For something like this, if probably hit up YouTube and search metal roof + roof boot or pipe flashing
Two potential options.
Option 1. More caulk. It’s possible that the roofer did put caulk under the boot. Perhaps they only put calk on the perimeter. https://youtu.be/eidzG74VT5U
And that said, when I’ve had problems with flashing and my roof, the best thing to do is to get into the attic while someone pours water in specific areas. That’s the fastest way to know what specifically needs to be fixed.
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.
The sealant is supposed to be that way. You’re supposed to bend the aluminum to the match the roof, put a bead of caulk under the boot, put screws at the major fold lines, and put a bead of caulk around the edge for extra protection.
I don’t know if the installer put the first bead on, but the screws are basically in the right places and the that finishing bead is there.
The problem might be because the installer installed this at a 45 degree angle. That’s not something I normally see. That forces the big bend to be on a corner.
I usually see these at that angle, supposedly so it sheds water to either side instead of damming it by being horizontal. Metal roofs are pretty common in rural areas, and the boots are done like this.
