build_common.ps1 has the following line:
Set-Content "$($this.xcomModPath)" "[mod]`npublishedFileId=$publishedId`nTitle=$title`nDescription=$description`nRequiresXPACK=true"
Which apparently makes mods compiled with vanilla SDK using X2MBC count as WOTC mods as far as various mod launchers are concerned. For now it's probably possible to set RequiresXPACK=false in the compiled mod, but would be nice for X2MBC to take care of it automatically.