Hello Anna,
Using qPCR to normalize amplicons is a good idea. I've heard this suggested before, but I don't know of a methods paper on this. If you choose to try this method, I would love to see the paper.
One possible way to combine these regions together in a single feature table is to perform closed-reference OTU clustering. While it does have limitations, it's definitely the easiest and simplest way to proceed. Might be worth trying!
https://docs.qiime2.org/2020.2/plugins/available/vsearch/cluster-features-closed-reference/
Colin
P.S. In this post, Lauren is also trying to analyze data from multiple regions at once. It's different regions sequenced, but it's the same underlying problem and could have the same solution.