If your question in this scenario is can a defederated Lemmy.3's posts reach Lemmy.1 if they're posted to a neutral intermediary (Lemmy.2), then no, instances that are defederated from each other don't trade information. Doesn't matter how far the post/comment spreads if your instance is ignoring it based on point of origin.
If both users subbed to a mutually federating instance's community, they would both be able to interact with Lemmy.2 users, but they wouldn't even be able to see each other.
As for bots......I fear there logically is no good way to tackle this because of the nature of the fediverse itself, short of blacklisting every baby instance and manually approving users. At the very minimum, asking for verified email and never auto-suggesting usernames, which is far from airtight but could slow them down.
Ideally, one could write their own bot to evaluate users for brigading behavior, copied posts and comments, etc., but that seems a little sci-fi when some instances barely have a working search bar right now