Yeah, I had a mini debate with Mr Do about this, and the conclusion was - as expected - that you can't please everyone. The reality I face is that I play on a 16:9 screen all the time. My screen is 52-inches, and it doesn't rotate, therefore my over-riding concern is for a Bezel and game to work well in that orientation. You can't really be all things to all people (well, I guess you could, but that would be a lot of work).
I chose not to be a slave to authenticity, and to simply deal with my own reality (non-swivel screen) and to concentrate on that. I'm working on the basis that a) having a Bezel is better that not having a Bezel at all times; b) Bezels are better designed in such a way that they recognize the 4:3 source, while at the same time look good stretched - or at least not so odd that it matters.
The creators of Mame are admirable in their quest for authenticity, but personally for me it's about the games rather than worrying about that side of things.
It's a case of - each to their own. I'm reasonably comfortable with LAY files at this point. However, my main goal is to have some artwork there when usually there's none. I'm not at all opposed to stretching the gameplay screen, as long as it's not so distorted it looks odd (which is itself subjective).
Since I'm producing a lot of artwork right now, the creation and suitability for 16:9 is a greater priority. Hence I am using templates, rather than - at this point - worrying too much about fine tuning every one. Once created I have all the artwork I'm using (the layers etc) to tweak everything at a later date if needed. This renders what I'm doing rubbish for those wanting authenticity at all costs, but adequate for those stuck with a non-swivel 16:9 screen.
I do however, take your point. If you want authenticity, and to allow for rotating screens (although in the case of a square Bezel, rotating the screen wouldn't make a difference for someone exactly replicating playing through a square Bezel on a 16:9 screen), then I guess it's easy enough to edit the LAY files yourself. My intention here was to provide a file that was simply a "click to download and use" for people who don't care about any of this stuff.
I do realize what I'm saying here is heinous in terms of Mame's goal. But just to be clear - speaking personally - I want original artwork, but I am more than okay with it being altered to get the most out of my screen. It's certainly enough to make a hardcore Mame user cringe. All I can say is - I'm at war with black bars, or at least ones that dominate the screen.