In The Next Generation episode “The Chase” it states that all humanoids come from the same ancestral species however the Xindi (which have six species) only some of them are humanoid. How does this work? Also which Xindi species are humanoids and which are not?
The "seed code" seems to push individual species toward a humanoid shape and size. This doesn't, however, preclude other forms being chosen by evolutionary pressure and natural selection. On Earth, for example, we see the earliest space-faring species arising from dinosaurs. Over time they became humanoid but they certainly didn't start that way. Perhaps, over time, the non-humanoid Xindi species will eventually become progressively more humanoid.
HUMANOID: (continuing) Our scientists seeded the primordial oceans of many worlds, where life was in its infancy. These seed codes directed your evolution toward a physical form resembling ours -- this body you see before you.
TNG: The Chase
That being said, we know that the seeding happened on a few planets (at least 19) but it's a very big galaxy and life has almost certainly arisen independently on thousands or millions of other planets unconnected to the progenitors.
They likely don't relate at all.
In The Chase, an ancient species seeded the galaxy something like 4 billion years ago. However, out of the thousands of worlds and lifeforms in the Enterprise's databanks, if not millions, only lifeforms from 19 known worlds contained their "algorithm".
COMPUTER: Pattern match found.
COMPUTER: The number blocks are mathematical representations of fragments of deoxyribonucleic acid strands.
PICARD: DNA fragments?
CRUSHER: Each from a different lifeform from nineteen different worlds.
PICARD: The planets that these fragments are from are scattered across the quadrant. No wonder it took the Professor so long to collect them.
PICARD: So, four billion years ago someone scattered this genetic material into the primordial soup of at least nineteen different planets across the galaxy?
The Chase establishes that the vast majority of known worlds and lifeforms were not seeded by this race, not all humanoid life. So the odds that the Xindi homeworld was seeded by this race is extremely low. Furthermore, this race lived and died sometime around 4 billion years ago, long before many contemporary worlds, including possibly Xindus, had the opportunity to form. The most likely answer is that they are unrelated.