I wouldn’t expect the new user silencing to affect users on TL3. And the last one won’t help with the TL progress either.
Which reasons do the mods and TL4 users select for their flags? I am not sure if it matters in this case, but I remember that for some features, flagging “spam” and “inappropriate” have more severe automatic consequences than other flags. In that case, a custom flag type might help. But it’s just an idea; I haven’t verified it.