Making this work is not really a "limitation". Bottomline has an archiving solution, they are in business to sell that solution. If they didn't have TCC then very likely they would provide tools to publish merged forms to other archiving solutions. Getting things to work with other archive systems takes some effort, and sometimes it just doesn't work.
In the case of the project I'm working on, LaserFische is already the solution. It's been in use company-wide for years and moving everything to Carchive is not a viable solution. That would be like reinventing the wheel. I know that in my case I'm going to manually configure things in LaserFische so it knows where to look for PDF's and how to map them (where the invoice number, date, customer name, etc. is located on the page).
Regarding writing merged PDF's to a folder, that functionality depends on the version you are running. Initially the only way you could get that was with Cemail. Then they added something called "PDF Publisher", which is a licenced product. I think the latest software (v6.4 with a patch applied) can write merged PDF's to a folder as part of it's base functionality (but I haven't tested that yet).
With all that said, I agree with Michael's comments. There is good and bad in every solution.
Karen.