Sorry to rain on your parade, but I've already been doing this in my mod for quite a while

The original idea was for my historical mod and that it would allow products to be improved over time by phasing out old manufacturing methods and bringing in new ones, but allowing for both to be used simultaneously for a period. The increased use of plastics after the 1950's was my inspriation to experiment with this. Obviously you need to create a few bridge products to make this work (ie you can't phase out steel entirely or any of the other staples) so you create a sub-step to give you that flexibility or you just use products that really did get phased out by better ones, like Bakelite for example. Using this feature was also going to be one of my core enhancements for the whole electronics piece, where certain manufacturing techs and materials simply become phased out over time and are replaced by better ones, thus allowing for a seamless transition over the years. A case in point was when adding the nine generations of console and for televisions, where not only the tech changed dramatically over the years, but also the specific materials used (a key feature of my mod is the number of detailed and very specific product inputs, which does make this a bit easier).
I've never been a fan of the customisation element of the game, and after playtesting with multiple manufacturing blueprint it was clear it was stable enough to be mainstream as a feature and would replace customisation for me. In any event it was useful to differentiate between distinct methods of producing and selling goods as an ongoing concern, not just historically and for phasing out - this was the enhancement I allude to in my Mod teaser ("mind blown"). I did actually mention I'd successfully play-tested this feature to you David on discord, but I guess it went under with all the other stuff we were discussing. I genuinely don't remember if I included one or two examples of this feature in my latest release, but it would have only been for a few products (I think Lager was one), as I've been largely holding the feature back for the big release which unfortunately is loooooong overdue now. The reason why people may have never noticed it until now is because you need to use the forward/back arrows to navigate between the multiple blueprints as the overview itself only shows one product per line and as discussed in this thread, the AI cannot use it as far as I can tell.
Brutus you did identify some of the issues with it as it stands, but these are actually not that bad and hopefully easy to fix - for one on the order of the recipes, in my game, the same recipe always shows first regardless of whether you start a new game or any time you load up, and if it were random this would not be the case, therefore there is certainly an underlying logic to it. I haven't exhaustively investigated this and tbh I don't remember as it was a while ago that I was playing around with it, but I'm fairly certain there is a way to affect it even if its not the order in the manufacturing file. I'll try to remember what it was.
Using the manufacturers guide when you setup a factory it does indeed continue to spawn the "first" blueprint into the factory, despite the alternate blueprint being selected. I would suggest this is one of the easier elements to fix though and was on my wishlist to ask David for with my 2.1 release.
One way to get the AI to use the alternate blueprints though is simply to phase one of them out (need bridge products for this as I said before). Not as elegant as I'd like, but it works. The bigger issue I found was that when pushing the envelope on these kind of design features, the AI rarely manages to keep up. David and team have made some enhancements over the last year though and many of my early mod features have now started to work a lot better, so I do feel there has been improvement on this front. I'm therefore hopeful that the AI will use this feature correctly as and when it is fixed.
Either way, I guess my secret is out now and its not like I had a copyright on it anyway....it is a cool feature and it definitely adds more flavour for the player, even if the AI struggles. I've been playtesting my mod iterations as I've been going along and having well thought through manufacturing options is really fun. In my current version for example its cheaper to use plastic bottles for milk, but I set the quality lower for the milk (by virtue of tweaking the numbers in the manufacturing sheet) and even though they are produced faster (by changing production speed), it is ultimately all about the fine tuning between the different elements in both manufacturing.dbf and producttypes.dbf. Modders will need great attention to detail if they add this as a feature as its not as simple as just replacing one material with another from a game balancing perspective.