@neauoire @furiousgreencloud I think it depends entirely on the client you use. The default Mastodon web app is already not very good at grouping and decluttering the notifications column, so, go figure how good it is at using multiple accounts.
I don't know if an actually good client exists, but algorithmically it shouldn't be too difficult to deduplicate timeline events. Mastodon already does deduplication on the server side.