Is there some way to configure the options such that stronger-than-vanilla enemies kick in only starting from mid-game? I usually play with 100x science multiplier, and I'd really love early biters to be easy, but late biters to be harder.

On 100x, it's a long way until tank/flamethrowers/artillery, so early biters are a big annoyance. I wouldn't want spitters/snappers from the start. But then once you research stuff, you actually have a lot of time for thorough defenses, and a bit more scaling past behemoths would be great.

Yes, it should be doable.

What I tend to tweak for marathon style runs, is disabling enemy scaling from time (both vanilla pollution and EvoTech research), but ramping up pollution based ones. This way enemy scaling will naturally follow the sprawl of your base and increase pressure as your production increases. For 100x though, I'd actually tone DOWN the pollution factor as well, since it takes so long to progress the tech tree.

So tweaks would be:
EvoTech - "Research points required" -> increase from default 100k. For 100x vanilla something in the ballpark of 500k should do.
EvoTech - "Research points from time elapsed" -> set to 0.
EvoTech - "Research points from produced pollution" -> set to 0.
EvoTech - "Research points from absorbed pollution" -> set to 3-4. Combined with above it will make pollution control relevant, scaling biters only when base actually provokes attacks.
Map settings -> Enemy settings -> "Time Factor" -> set to 0.
Map settings -> Enemy settings -> "Pollution Factor" -> set to 5.

That should shift enemy scaling more towards rear end of the playthrough.

For reference, I'm at 250 hours in my K2 x5 science cost run, slowly building 1800 SPM endgame base while 120 SPM "green" starter base is churning through optimisation science. Evo at 98%, with EvoTech scaling putting Legendary Behemoth Biters at 8500 HP and 1k+ damage per hit. Settings are:
"Research points required" = 250k
"Research points from time elapsed" = 0
"Research points from produced pollution" = 2
"Research points from absorbed pollution"= 5
"Time Factor" = 0
"Pollution Factor" = 15
"Enemy Rebalance" = ON