I use butyl tape for quite a bit of my bedding. It does what I want: Easy to apply, stays pliable for decades, easy to remove when you want to (that last is something I really appreciate). Essentially, I use butyl unless there is a reason not to.
Reasons not to that I have encountered:
1) Fuel fills (it's not fuel resistant).
2) I want something gunnable (such as when I did the rub rails in place).
3) I really want something that looks white (3M4000)
4) I need an adhesive not just a bedding compound.
One caveat is that I have found that butyl tape quality varies widely. I had some "good old" ancient stuff from way back on the parts shelf that was brilliant. Never could duplicate its properties until I started buying "Bed-It" from Maine Sail. It's just like the old stuff. Nothing else I bought was nearly as good (much less elastic, didn't hold up, etc.).
Some of the "good old" stuff on my camper which was built in 1975 was STILL super flexible and doing its job when I went to remove hardware in 2009.
PS: I did use butyl tape on all my cleats and most other deck hardware. I didn't use it on the rubrail repair because I didn't totally remove the rubrail and hence wanted something gunnable. I used 3M4000 and a caulk gun. I used polysulfide on my fuel fills.