For me, Mechanical keyboards cause fatigue as the key travel, regardless of which flavor of the key type, is too much. I prefer using Apple's new magic keyboar with numpad. It has a 1mm or so travel and feels fantastic.
But! There are low-profile switch mechanical keyboards now, and they're very similar to your keyboard. They're still a little hard to find if you want customization (like a preferred switch type).
Mostly they use Kailh switches, not Cherry MX but you probably can't tell the difference.
It's noisy, though.
For me the tactile feel is actually less fatigue as I'm not bottoming out like I am on low travel keyboards, I usually don't bottom out with them. I do know some that hammer on theirs and it gets crazy loud.
There have been a handful of IBM Thinkpad keyboards I didn't hate, but generally don't like laptop and low travel keyboards... I did get used to my ~2010 macbook pro kb eventually, my mid-2014 I don't use much and won't have it anymore at the end of the month.
No, it's not just you. I prefer short-throw laptop keys, which require less distance and less pressure.
I use a USB version of the ThinkPad keyboard at my desk. (And I personally prefer the older version that includes a trackpad.)
I'm considering the Tex Shinobi mechanical trackpoint keyboard.