I use it in this manner all the time and works great.
I use an old program called pocketsense, which I modified a bit, which goes out to multiple institutions, downloads from each in ofx format and then combines them into single ofx file to import it into gnucash. Literally speaking they all are concatenation of individual files into one. It has been working fine since version 3.5 (or earlier I think).
Only hickup that I see now and then is If transaction are across two accounts (example a transfer) in ofx then gnucash doesn't cross correlate them but if that happens then I disable import for the "seconds" account, finish first import and then perform second import of the same file and then it cross correlates automatically. Nice thing with ofx import in gnucash is that you can import same file multiple times but not get duplicated entries for the same transaction.
I have tested combined ofx file that has investment account, banking account and a credit card account and if anything it is one of the robust feature of gnucash, IMHO.
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