Well hello, hello
I'm so glad you asked. Yeah, silicone is bad for a number of reasons, IMO. First of all, it's not that great at doing the job at hand. Second, as Scott mentions, have fun ever removing it, and even when you can't see it anymore, the residue left behind will make adhering anything else nigh on to impossible for, oh, a thousand years or so. Seriously though, some boaters have resorted to grinding the gelcoat off just to get rid of it. There isn't much I can think of that I'd less like to see on a boat, RV, etc.
So, what TO use? There are a number of options, and sometimes one or another product is clearly a big benefit or a no-go, but oftentimes you can choose amongst a few.
Butyl is near and dear to my heart (but only GOOD butyl*). Why do I like it so much? It does the job extremely well, lasts darned near forever (both doing the job and on the roll in storage), doesn't make a mess when you apply it, and -- best of all -- is an absolute cinch to remove when the time comes (and it often does come: A part you bedded in place breaks, you want to upgrade, etc.).
But butyl isn't right for everything. One, it's vulnerable to fuel (not a big deal on an RV, but you wouldn't, say, use it to bed fuel fills on a boat). Two, it can continue to ooze out a bit for awhile, and also would prefer to be tightened down slowly, over a period of a day or a week. The "ooze" is easy to clean off, but still there are cases that wouldn't work. Also, it is not an adhesive: You want to use it on things that are also mechanically fastened (screws, etc.).
Another choice would be polyurethane. Examples are 3M 4200 and 5200, Sikaflex 291, and others. These are adhesives and caulks together. That can be good or bad. I've had a crew just about tear the transom off a boat trying to get a broken swim platform off (it was stuck on with 5200). There are a few times that level of adhesion is needed, but they are very few. 4200 is still quite adhesive, but not as much as 4200. But they have their downsides too. One, they can be messy to work with, two, they can be hard to remove, and three, they yellow in UV light. But they do set up "permanently" which can be an advantage in some situations (it takes a while though).
Polyether is another choice (3M 4000). It's in some ways similar to polyurethane, but isn't supposed to yellow in UV light. I've only used it a half dozen times (on boat stuff), and don't have long term experience to speak to how it removes, etc. (has only been on four years or so).
On the "stuff on top" phenomenon: That one puzzles me. As Scott says, it's the RV standard. You bed the item (i.e. product of choice under the flange), then fasten it down (okay, so far so good), and THEN pour a bunch of self leveling gumbo over the top. You might for good measure run a bead around the outside too. It seems strange to me because that is never done on boats, and heaven knows they take on a LOT more water (solid water even, not just spray) than an RV, and they flex in a seaway as well. They can also sink. On boats you bed under the flange, then use some sealant under the fastener heads (but clean it off after you tighten the fasteners). In the end, basically no sealant shows. Nothing to trap dirt or debris, no globs. This even holds true for fittings beneath the waterline. The only time you'll see sealant on top of a fitting on a boat is when someone has a leak for some reason and they try a band-aid fix. But before long they'll remove the fitting and do it the right way, because it never really works (boats can easily last a half century or more, so things do get re-bedded a few times through their lifetime).
I suppose partly it might be that the flanges on many RV things are thin and flimsy (I'm looking at you, Fantastic Vents - although it's not just them). That makes it harder to bed properly under the flange. Also, on some RV's (not ours), you can't chamfer fastener holes under the flange to accept a "ring" of sealant -- but you can on our gelcoated/fiberglass.
Anyway, hopefully not too much information.
BG
*I have tested a number of butyl products and have only found one that has measured up to the "good old" stuff I have from decades ago that is still pliable, and still stretches feet without breaking. The others looked like butyl, but were more like putty or clay when put to the test. The one I use is called Bed-It. Basically, a fellow sailor found the same thing I did, but he went to a mfgr and had them start making it to his specifications. Great stuff! And it lasts forever even on the roll (which you can't say about the things in a tube, especially once they are opened).