I already request from them but they said it should be done on Waystones side.
hotsu0p/Trek-Issues#13 (comment)

Waystones only adds its structure to vanilla villages (and Repurposed Structures' ones which support pool additions through its own system).

Until Mojang adds a way to add structures to existing villages, villages from other mods or datapacks will not be supported. Instead, compatibility data packs can be created to manually add the waystone structures, as was done for some other world gen mods.

Hi, Trek developer here, wanted to ask a few questions.

1. If you would like to make our mods compatible i can help with that from our side.
2. I see there are 2 options how to make that work:

• either it is added inside lithostitched folder (i don`t know actually how that system works, but i can guess thats injection to vanilla villages houses pool)
• or by adding jigsaw that will spawn waystone in town centers of Trek villages
  I suppose first variant will be better
  Correct me if i`m mistaken somewhere

I'm not super familiar with lithostitched, but I imagine it would be possible to include lithostitched data in your pack to have it conditionally inject pieces into your villages if Waystones is present. That way, users who have Lithostitched, Waystones, and Trek installed together would get waystones spawning in your custom villages.

The alternative is having an additional "Waystones x Trek" data pack that specifically overrides the jigsaw pool in Trek to include waystone pieces.

Wait, you already have lithostitched folder inside you mod in data/waystones folder, don`t you already use that to inject waystones to vanilla villages?

The Lithostitched files shipped with Waystones were provided by the Lithostitched author and are only used if Lithostitched is installed alongside Waystones - the regular waystone piece injection done by Waystones happens in code rather than data, independent from Lithostitched.

Basically, Waystones' injection into vanilla villages is pretty basic and may not always enforce a waystone to spawn, but Lithostitched is smarter and can actually enforce it, so that's what those files are for, as an optional enhancement for players who have Lithostitched installed.

Oh, makes sense, thanks for explaining. I see you are not really updating your mod for older versions (like 1.19-1.20). Then i guess it will be my problem on making it compatible. If i get any results on this i`ll write it here, it will take time.
Have waystones changed over versions? I mean waystone blocks themselves. If i save it in 1.19 and load in 1.21 in structure block for example, will it break?

Yes, waystones NBT/blockstates changed in 1.20.1, 1.20.6 and 1.21.