What? EG's isn't really that good at Lotus, DRX just isn't that good either. They're definitely better at Split and they've literally banned Lotus. Also, your assumption is that PRX just auto-loses Fracture, but that's not how games work. Sure, EG has the best fracture but picks and bans are about assessing risk, and PRX might feel like they have a better chance on fracture than Haven.
EG has a lot of footage of their fracture, thus giving you things to anti-strat. Whereas their Haven has relatively low footage, and their form on that map is unknown. This really just comes down to how PRX feels about their Haven which I can't know for sure of course, but if they do not feel confident enough on it, I don't see why they'd pick it. Also also, fracture not being their top 2 maps doesn't mean much when your map pool is good. PRX fracture is still really good, and they could definitely beat EG on it if they're feeling it.