I noticed that manual journals get flooded by entries that I did not do "manually". A lot from those I recorded via the Bank Accounts reconciliation are also reflected there, even when I did not use manual journal for it.

It's best practice that Manual Journals only contain those that we journalised "manually" and mostly shall be non-cash transactions.. Cash transactions are supposedly recorded directly from verified bank statements or bank feeds — not through ad-hoc manual journals.