We spend a lot of time detailing bottoms with every jet install. I have only worked on a few V-drives, and never a strut.
If your V-drive guy didn't give you specific instructions, I have a few thoughts:
When you are setting the strut, some epoxy will ooze out. It is easier to scrape the excess before it hardens than it is to sand it off later. A few minutes of scraping before it cures will save you hours of sanding on your back.
Mix a little more epoxy than what you will need. Fill all of the voids between the strut base and glass so that it can be blended smooth.
You can manipulate the epoxy with wet fingers and it cleans up easily with a wet rag. Beware, water will make it kick faster.
If you are working under the boat, beware, it will sag. If you have a thick cross-section, such as in the front of a jet intake, it looks perfect when you walk away. Come back a few hours later and it has run down the street and robbed the liquor store.
The flats that I have been involved with, the strut bolts were not epoxyed in. I would assume because you have to check the torque on a regular basis. It's probably not a good idea to epoxy over the heads of the bolts like we do on the jet intakes.
Bottom line, it won't hurt anything to blend it for reduced drag. Afterwards, give it a coat of primer and some bodyman-in-a-can. Then lightly sand it front to back with 80 grit.
