with the hiding, whistlestop does not clutter the menu at all. One more category (50 is mainly due to stack size) would already help alot as it compensates 3 tiers. To reduce the size even on the machines, you can just define, that overtier 1 and 2 have normal recipes only and overtier 3+ has only the big recipes. (this resolves issue A and B)
In Whistlestopfactorios the big machines can only do the big recipes and all normal assemblers and handcrafting only the normal ones, hence you see no difference in how crowded crafting menus are.
A 2nd tier of recipes will create another problem. Already with 50 per recipe, you can create 3000 items per second. Max belt speed is 180(?). Hence it will already be tough to move. If you add another category of e.g. 2000 item recipes, you end with an output of 120k items per seconds which cannot be handled by belts and also not by stack inserters anymore(unless some super weird ones and than you need lots of robots or cargo upgrades). Or you need to add alternatives ways of moving stuff around.
Lots of lists for each of 5,10,20 and 50 recipes are pointless. If you cap speed at the the 1 recipe, you can also craft 50 in less than a second, hence no need for the recipes between 1 and 50. Only reason would be to adjust them to the overtiers. Hence create a special set of recipes for each overtier, overtier 1 gets 4xrecipes, overtier 2 gets 16xrecipes. This way building times always stay fine, but
Just to warn you about what I read in the code of whistlestop: Seems to be a big problematic with stack sizes at all. He reduced some recipes to only 10 items per recipe (e.g. some buildings), because internal logic seems to only allow one stack to be produced.
I also really like, that whistlestop searches all recipes to make big recipes. Found also another mod, which just hard coded all vanilla recipes into x100 recipes. Hence you miss all modded recipes, this is not the way I want it to work ;-)
I would suggest to make just a single extra recipe tier. But code it in a proper way to adjust it. But option 1 would be enough for the beginning until one can decide how to handle input/output.
I played a whole game with Whistlestopfactories and already these struggle with being limited by input/output issues, as they only have like 16 output lanes (+- a few).
If you just want to have a look at whistlestopfactorios, you can even add it to an existing game (the big factories only spawn on new chunks). The only problem is, that it messes up with some spirite sizes which sometimes creates conflicts with other mods. (just playing industrial evolution and it does not work there, tried to exclude all factory based stuff and only keep the 50 recipe from the mod did not worked out for me. Once it does not crash anymore, it also has no more big recipes (you can also see them in FNEI))
Maybe have a look into his code to see how to hide stuff etc