Just a general warning. Enemies scale every time you fly through a tunnel (HP increase). On Terminal difficulty, it is extremely noticeable, where the durability of everything roughly doubles after every flight through a tunnel and after flying through 2 or more tunnels, all enemies become ridiculously tanky and buildings take forever to destroy, to such an extent that the game can be considered unplayable on this difficulty, because there are several levels where you have to fly through multiple tunnels.

I finished the game on hard, where the scaling is present too, but much less severe (you have to fly through about 3 tunnels for the enemies to scale like one tunnel on Terminal difficulty). No idea about the other 2 difficulties.

I am not sure if this behavior was in the game back then, but it seems like a bug to me, so keep this in mind when playing. Don't enter tunnels too soon and don't fly through them too often, lest the enemies become too tanky to continue. Clear whatever you need to on the surface first before diving into tunnels. Every time you enter the yellow dot on the map (tunnel), it counts for the scaling purposes. So if there is a tunnel-cave-tunnel, it counts as 2 tunnels.

Also, the scaling seems to be percentage based so it gets exponentially worse with every tunnel. Assume that on hard difficulty an enemy has 10 hit points and HP increases by 35% every tunnel, it goes 10, 14, 18, 25, 33, 45, 61. So after 4 tunnels, enemies will have more than triple the normal durability. Now imagine a building that has 200 HP instead of 10 and see how it gets bad very quickly...

For Terminal, make that like a 60% increase per tunnel and it gets ridiculous very quickly, even for enemies, not to mention buildings, where you will end up having to shoot into one constantly for 4 minutes to destroy it.

And final note, the only thing that does not scale are enemies inside the tunnels themselves (they always have the same durability). But everything else (even bosses) scales.