Hi there!
Wake to sleep is done so that LO doesn't wake at all. The technique "resets" their sleep cycle and helps to get rid of a habitual waking. It's up to you if you want to leave him for a while to resettle. Some LOs will on their own.
However, all of that said, I think your little guy is actually taking undertired naps. This means that his body doesn't feel tired enough to go to sleep after only 40 minutes, and can result in fighting the nap (check) and 45 minute naps (check). At 6 weeks, the average A time is ~1h to 1h15. I would wait until the 50min/1h mark and then do the wind down...you might be surprised
Give that a shot for a couple of days and see how he does.
If he suddenly jumps to 30 minute naps and fussing/crying upon waking, then it was probably too much A time (every baby is different so it's really just learning what works best for your LO). If you get a kind of nap shorter than ~1.5h, then reduce that following A time by 20-30 minutes to avoid OT at the next nap.
Hope that helps a bit
Keep us posted!