Update:
So, I submitted a ticket and got back a response from Wiim. According them the culprit is my phone microphone which is not accurate in the lower frequencies. I also shared with them the new measurements results with the mic and waiting for response.
I suspected that also, so I ordered a Dayton Audio iMM-6C microphone and I redone the measurements.
With the mic the sound is totally different what I used to in the lower frequencies. It's less boomy more accurate, put together. Kinda miss more bass sometimes.
The sub speaker sync is went from subwoofer delay to speaker delay. It now consistently measures between 8ms - 10ms delay to the speakers not like before. Also I did measurements with phase 0 and 180 and it was in both cases 8ms to the speakers. Also, I did room correction with 0 and 180 phase but the 0 phase sounded off in the bass. I was listening the same music and with phase 0 the bass sometimes missed, like on and off it was weird. I stayed with 180.
Oh, and the dip around 100hz is less obvious with the 180 phase.
So, currently I'm getting to used the less bass in my system but probably I'll ending up EQ a bit for more bass.

Here are my measurements with the calibrated microphone.