It seems to me that the main advantage of plastic food storage containers over glass ones — other than price — comes mostly from weight. You don't want to carry your leftovers to work in glass containers; they're heavy!
(And AFAIK no other container material besides plastic is a good substitute for glass in food storage, because 1. they're not washable / interact chemically too much with the food, or 2. they're not visually transparent enough to tell what's in the container. So let's ignore other materials as possible solutions for now.)
I presume that the problem here isn't that microwaves are causing vaporization or spalling of the container material in such a way that microplastic particles coming from the outside of the container can end up in your food. (If that's the case, then plastics are basically entirely screwed for this use-case, and we may as well give up on them entirely.)
But presuming instead that the problem is only with your food interacting with the inner surface of the container, under heat/acid/etc — i.e. some kind of leeching or osmosis of the food against the container surface, causing the plasticizers in the container to "exchange" out...
Then, if that's the case, would it be possible to make a food storage container that's mostly plastic, but then has "just a little bit" of glass, lining the inner surface? A glass barrier-layer, sort of like how plastics themselves are used as a barrier layer on the inside of aluminum cans? Resulting in something that's a lot lighter-weight than a thick glass container, but a lot more "inert" than a plastic container?
Glass is usually brittle, I know; and unlike a glass food-storage container, which is usually thick, plastic food-storage containers are usually more thin and flexible. A plastic substrate would want to bend, and that would, naively, shatter a glass "film" on its surface.
But! We've recently invented bendable ("foldable") glass, haven't we? And in fact we're laminating this "foldable" glass to plastic substrates all the time. It's even transparent!
I think it's workable as a process. You could, in theory, produce glass-lined plastic food storage containers. I only wonder if it could be made cheap enough that, even at massive scale, these containers would come out at a price-point that anyone would pay.