What is happening in real life is not what you think it is, don't compare this game to real life. In real life bullpens are massively overpowered not because of "tired players" because that's not actually a thing, it's because average bullpen velocity is substantially higher than average SP velocity, and also managers go RLRL much more frequently
On HBD, velocity = strikeout rate as opposed to literal MPH, but it is calibrated to the historical average as opposed to recent trends. In the past 20 years, MPH velocity has exceeded the threshold of human reaction time, so against a guy like Chapman or Kimbrel, hitters are up there guessing basically. Close your eyes and swing as hard as possible. Their K-rates are not calibrated from 0-99, they are hilariously off the scale, they should be topping out at something like 175-200 or more
There's nothing you can really do, it's just the way baseball has historically been versus how it operates recently. Your guys are going to get tagged sometimes, lower their pitch counts and raise their Call Bullpen