I don't profess to know it all, but in over fifty-five years of flathead building, I usually remove the bolts and install studs. I'm sure other will have something to say, but that's what I have done for all these years.
It can be done - as long as you have the correct length for the type of heads you're running. With that said, you're usually better off running studs - as the co**** thread remains in the block and you're tightening and reading the torque values on the fine threads. This gives much more consistent torque readings and provides better clamping forces on the head. On all my hot-rodded flatheads, I always use studs - high quality ARP stuff is the best.
I used bolts in an older flathead. It works. The use of studs is probably better I just have memories of heads stuck on blocks because of the studs. Now, if I can get the bolts out, the heads will come off. I went to Caterpillar and bought the bolts. Neal
studs are better from a technical point of view. that said if you ever tried to get aluminum heads off that have welded themselves to studs you mite prefer bolts as i do...
Studs are more efficient, bolts are more convenient. Your call! I think the heads are different thicknesses, the stock bolts won't all work on a head made for studs. I recall many hours struggling to get heads off when they seize to the studs. Not fun!
A big issue...like all OEM engines, the decks on a flathead would be better if thicker, both for strength and for extra thread depth. Your 21 stud threads are 70 odd years old, and have been subjected to rust, repeated rebuilds, etc. Flatheads want multiple retorquings...studs allow the threads to be set in sealant and fully straightened to vertical during the build, then let entirely alone...all the frictional wear and stress of retorquing happens upstairs on the fine threads.
I used 8ba bolts on my flathead due to the thickness of the heads. I cut the heads of 4 hardware store bolts to use as guides and put the heads on. Than put each bolt in with Idian head shalack. Of course you take the guide bolts out and put the correct bolts in. There just to hold the head on till you get a few in. Worked for me. Good luck!
One thing to mention if you use studs, say in a AV8 set up, it might happen you have to remove the steering column to lift the left head. Even worse with extra thick alu heads. No big deal with bolts........