Flat mount brake caliper and rotor tolerances
tldr: my road disc bike has tight clearances too and nothing rubs, so "it works for me".

Tolerances are always hit and miss, especially when multiple parts are involved like with fork/caliper/hub/spokes/rim/rotor combinations. That's a lot of parts to multiply tolerances by. There are no standards for caliper to spoke clearance besides what original manufacturer deems appropriate. Some calipers might protrude further inside than others (TRP Spyre is notorious), some do not.

Here's some personal experience: my road disc bike has less than 2mm clearance between caliper and spokes, both in the rear (Hope RX-4 caliper, post mount, 140mm rotor, bladed spokes) and front (RX-4 flat mount, non-stock fork, 160mm rotor); rotor to fork is about the same; this did not cause any issues as of yet. To compare, clearances on my MTB are a tad bigger at ~3-5mm.


  Here's my question: since I have no other disc brake bike to compare,
  is it normal to have such tiny clearances on a gravel bike?
  My original project would be using a 140mm rotor, will it rub the
  spokes when pedaling out of the saddle or climbing?


Nobody can say for sure, it depends on various factors like your weight, pedaling style, power output, frame stiffness, if rotors are true or not, how stiff the wheels are, etc. You might want to confirm that no interference happens to be sure, but I think clearances you describe are on the lower end of acceptable and as long as nothing rubs in stand the bike should be fine.