Given these objects come from a bigger script, I’ll skip questions/suggestions about how this bridge surface is initiated.
After checking a few options with what you have at the moment, a rather silly one is to generate tween curves between the two edges constituting the bridge surface, pull and loft, then join all breps into one - no tolerance-tweaking* required:
MergeFaces2_cheat_rc.gh (117.8 KB)
*of course the tradeoff is ‘losing’ the original bridge to this new one.
For that matter, a better ‘clone’ results from more tweens:
Just keep in mind it comes at a cost, above 20 tweens things can get a little slower.