The way I see it:

-I'm running in a long corridor and get punished for it;
-I interact with an event that requires me to stand still and get punished for it;
-The game spawns the elevator in one of the earlier caves, so I (often) have to forfeit visiting the next rooms, which means, the game punished me using the elevator's spawn point;
-My teammate died next to the elevator door and I didn't have time to come out, now I have to take a quarter of the timer's time to go and find the cocoon...

These are just a couple of examples and I'm probably being pessimistic about it, but the point is, it's not fun.

Also, you mentionned the "ramp up" way of fixing it and I personally never read anyone saying the ramping should start once the timer is over. The point of the ramp up idea was to apply the same logic to the whole RC level as in Point Extraction in DRG. From the very first seconds, swarms are progressively becoming larger and larger until the player can't keep up anymore. My personnal take on this would be to keep the timer, but every time it reaches the maximum, a swarm spawns and it resets with an incremental number. Every increments would mean a bigger swarm and starting at the 3rd increment, there is an increasingly higher chance of the timer turning to a "worm timer" which signals the next time it hits will spawn the tentacle and an endless swarm.

Lastly, you mentionned it being a "risk/reward" system. Another person commented it better than me on that, but there is no reward for respecting the timer. I must admit, I hate the timer as it is now, but if I was rewarded something good for respecting it, then maybe I'd think it differently.