Interesting. It's hard for me to visualize... but are you saying the bead lifts up the "base guide"... filling in the "gap" in my second image? In a perfect world this would solve the problem (as would shimming with tape or something else), but the real issue is how much do you shim? Or in this case, how much do you push the bead out? It's all happening at such a small scale you can't trust your eye. Too much shim (or adjustable bead) or not enough, and you don't solve the problem... you could even make it worse with way too much shim.
Or maybe I'm misunderstanding what the bead does.
In the product on amazon I linked, the bead is the brass object in the center of the guide. Basically, it's a round brass "bead" that is non concentrically mounted. It just as acts as a bearing surface on the base edge. Since the bead is non-concentrically mounted, as you rotate it, it lifts the guide so it files the base edge away at an increasing angle. The bead has several "snap" stops built into it so it stops at predetermined angles of rotation, each one corresponding to a different base edge angles (increments of 0.5, starting from 0.5 to 2.5 degrees). Basically, they've done the geometry for you and the once you snap the bead into 0.5 degrees, the bead will lift the guide to file the base edge at that angle.
Very good point. Until the base guide sits flush (and the edge step is completely cut out), you are cutting a smaller angle than you want, which leads to an acute "base-side angle" (assuming 90 degrees was your goal). I agree with your reasoning for obtuse being preferable... adding to those reasons that an acute angle is probably grabbier, in a bad way.
Some people do ride with an acute angle, say 2.0 base / 1.0 or 1.5 side edge to achieve an 89 or 89.5 degree edge angle. Based on my experience asking people about their setups, I've heard of angles all the way through 88.5 to 88.0 being used. From what I gather, you would not want such a corner angle if you are riding hardpack and aren't bombing big mountain deep powder. Even an 89.0 would be necessary only for real free riding. The effect of an acute corner angle is cumulative with the base edge being shallow as well (0.5 or even 0.0).
I prefer a 90.0, 90.5, so I would set 1.0/1.0 or maybe a 1.5/1.0. I've tuned old boards all the way to 2.0/1.5 and 2.5/2.0 and it gets a little sketchy on hardpack which is what most transitions and landings are coming off jib features in East Coast parks. It's incremental, but noticeable.
Still trying to figure out exactly how that tool works to solve my problems, but I am definitely open to buying a "base only" tool... even though I did invest $60 in my multi tool.
And yes, 1.0/1.0 is my goal and I believe what my edges are already set at. I just want to do a very light filing at that setting to confirm it, and after that move to stones for the long run.
I take the approach that each deck is slightly different and handmade, the edges may not be set flush or matching angle to the base surface as other decks. I just tune it at increasing angles (base edge first, then side edge to keep it from exceeding a 90.5 or 91.0 corner edge) until I find a set that I like. I'm not so much worried about the edge sets angles in an absolute sense - I only care that I can deduce what the final corner angle is using the angles. If it happens that it's 2.5 degrees on the base an 2.0 degrees on the side edge feels right, then that's what I use. It doesn't bother me that I might have 0.5/0.0 on another deck. Even with a good set of vices, a steady hand and experience, setting an edge angle is more of a feel type excercise, than a precision machining one. This is why I tune my own edges and if I didn't, I would try to find one particular shop and use the same guy. I highly suggest using the "sharpie method" too - color the edge you are setting with a permanent marker and make sure you completely remove the surface.
Once I set my angle, I don't ever tune it again. I only use the file guides to take a light pass at the surface if it becomes extremely coarse. But I prefer just using a hard gummy stone because it is better at taking the coarseness away while minimally affecting the edge set. Note that I ride almost primarily freestyle and racers or alpine enthusiasts will find edge tuning and maintenance to be a much more painstaking task.