It’s not that bad. I have three accounts in one PP file, let’s call them: Personal, Joint and Retirement. Each has accounts for: broker deposit, broker security, and bank.
For each, deposit funds into broker deposit which is used to buy broker securities and pays dividends into bank. I can report on all, or most reports allow filtering.
The only issue I have is with income when the same security is held by different accounts: CSV import of Portfolio Transaction does not work if ISIN is not unique - #9 by flywire
This has nothing to do with taxonomies.