You are overthinking the issue.

It does not matter where your flight arrives from, it matters more which passport you hold.

Any US or Canadian passport holder with a biometric passport is now able to use the e-gates that were previously only available to European passport holders with a biometric passport.

Upon landing, if you are lucky enough to get a gate you simply proceed to passport control and the e-gates with the flags of the permitted use passports are displayed at the start of the line. If you are unlucky and get a remote stand, the bus will arrive right below passport control and the exact same e-gates are there. LIS is not a huge sprawling airport, there is only one passport control for arrivals/departures which is part of the bottleneck mess at peak times.

As others have already mentioned, once you have exited e-gates and have your passport quickly stamped, you will see the security lanes that to enter the Schengen Zone gates area. This is the second potential bottleneck area, but when I passed by at 720 am roughly it was quite empty which surprised me.

Bottom line: for US/Canada passport holders with biometric passports that are arriving from non-Schengen destinations, the use of e-gates makes things much, much less stressful and exhausting. A connection time of 45 mins could be possible, but I like the 90 mins just in case.