Yeah, well that can be a double edged-sword. I've been there, done that & know what you're talking about. BUT if you ***** up the bead you can wind up with anything from a minor to huge vacuum leak that's impossible to fix w/o yanking the entire assembly a second time (something that guys who *hate* to sink a distributor cringe from) and I'm just not sure it's worth it. The rubber piece CAN get sucked in or pushed out if you don't set it correctly but 9-times-out-of-10 it works just fine. When it *does* fail it's usualy because somebody made a mistake when installing it, the gasket system ITSELF works just great and factory mechanics have been using this style of gasket for *decades*. The rubber end-pieces have small rubber "pins" that stick down from the bottom half, these will line up with the small holes in that section of the block gasket surface. Run a *small* smear of silicone on the surface of the block to help secure the bottom half & be sure you get the pins into the holes & then use your finger to smear a thin layer of silicone across the top of the rubber piece to help secure it to the intake. Make sure you put a small blob of silicone at each of the 4 corners where the regular gasket meets the rubber gasket (this part is really important, so be sure to double ck) IF you TAKE YOUR TIME and do this right you wind up with a seal that will last 10-20 yrs. After trying the "thick bead of silicone" method a few times (and really, I have, I've tried it 5 or 6 times) I much prefer to take a few minutes and do a good job with the factory gasket set. I went this routa after having a professional race shop assemble a 460 for me this way. I got the truck back, drove it for two weeks & then took it from Mass down to New Jersey for 22wks of Dive School, got down there & realized my oil was reading 2-3 qts HIGH and it was looking like chocolate milk. The big-gob or silicone gasket had failed and I was leaking anti-freezen directly into the crankcase. Had to pull the manifold, clean everything up and reinstall a set of *proper* gaskets 600 miles from home using the tools I'd carried with me. NOT something I'd like to do a second time and ever since I've taken the time & had the patience to properly install the correct factory gaskets.
Without a doubt all sorts of people will have their own ideas on this based upon their own individual experiences. Read & evaluate them all & then make an informed choice of your own.
Also, make sure to reinstall the valley pan. Some guys leave this out for some strange reason. Reinstall the damn thing, having "extra" parts left over after rebuilding something is NOT a mark of genius. I absolutely guarantee that you (or someone else) DID NOT re-engineer something like this on the fly and suddenly improve it. Reinstall *everything*