None of these things should have happened if transporters are portrayed on screen as they're supposed to work in the various non-canon technical manuals and dialogue etc. We've never seen biofilters do much of anything (apparently the Reliant's didn't even filter out Ceti eels, despite Strange New Worlds establishing that TOS era transporters already had biofilters).
Strictly speaking, the moment Picard was transported the first time after his recovery from the Borg, the transporter, which has a data log of the person being transported down to the molecular level, should have issued a warning saying, "DNA inconsistencies found in relation to previous instances of transport. Medical evaluation is highly recommended" or something to that effect.
Basically, if transporters operated as we're told in dialogue they operate, with biofilters, etc. the villains' plot in Picard would've been foiled in like the 2nd episode of TNG Season 4.