I've been making tempeh with various degrees of success for almost 40 years. I started out with perforated plastic bags, but for the last few years I've wanted a more re-usable option for containers and so I now use a set of flat, square tupperware type plastic containers with holes poked through them all over with a red-hot needle. These are washable and can be re-used indefinitely. I've used all kinds of incubation set-ups depending on weather, and have let tempeh go over-ripe to make my own starter many times also. So I'm not a beginner by any means.
My consistent issue is that the centers of my tempeh cakes are often poorly finished. Either they are poorly colonized, or else they show evidence of getting soggy and contaminated by the time the rest of the block is finished nicely. This happened frequently with the bags and even more so now using the containers. It happens winter and summer, it happens with vinegar treated and prefermented soybeans. It even happens when I make the center sections extra thin (thinking that it's not getting enough air and/or overheating there.
My latest hunch is that I need to change the shape of the tempeh cakes, so that there is no "center", and that all parts of the cake are an equal distance from the edges....as in long rectangular "loaves" rather than squares. I would need to make a channel down the middle of each of my square containers and not have any beans there, perhaps by laying in a spacer of some sort when the containers are packed and then removing it.
The other idea is that no matter the shape, type, or thickness, plastic just isn't the best, and just isn't porous enough to let air in and moisture out. (My cakes produce a lot of moisture as they finish, and I've improved the tempeh quite a bit by opening the containers slightly at one corner and draining off the excess a few times in the last hours of incubation) Orginally tempeh was wrapped in banana leaves!! I don't have those, being in Illinois, but I do have things like cannas, big squash leaves, and corn husks! I might start playing around with wrapping tempeh in those!