I don't think that's all that strong. It's reasonably well-known that processes such as heating, drying, canning, and so on tend to reduce the nutritional value of fruits and vegetables - such as vitamin B and C, sulfurophane in broccoli, antioxidants in blueberries, etc. A quick google should reveal a ton of studies. So it might not be surprising that extracts have these kinds of issues as well.
I think OP is probably right that these meat substitutes are less healthy than eating veg in its raw form, but perhaps the question should be how they stack up nutritionally against the red meat they're replacing.
Yes, but not all processes destroy nutrients. Frozen vegetables are just as healthy as fresh (possibly more so). And it appears whey protein (in essence, protein extracted from dairy sources) is very healthy; again arguably healthier than an equivalent amount of protein obtained directly from "raw" dairy sources (cheese, milk, etc.).
Obviously pea protein will be missing out on some nutrients found in the parts of the pea which were discarded, so may not be as healthy as raw peas, but I understood OP to be saying that pea protein may be actively unhealthy, and indeed, that anything but unprocessed "whole" vegetables is unhealthy. That's seems unsupported by current science.
I think OP is probably right that these meat substitutes are less healthy than eating veg in its raw form, but perhaps the question should be how they stack up nutritionally against the red meat they're replacing.