The canon Craftworlders have just as much reason to hate the Dark Eldar yet work with them militarily on occasion, there's cultural crossover with Craftworlders who can't manage the Paths becoming Dark Eldar and vice versa, and there are apparently many smaller realms in the Webway where you can find all flavours of Eldar (except Chaos) trading with each other for the goods and services only the others can supply.
And there are also the Harlequins, one of whose self-appointed jobs is to mediate this relationship and act as intermediaries when required. We don't even have to so are our process with them directly, the Harlequins would probably be the ones who did the bulk of the actual sharing of the knowledge to the various Webway realms.
Also, while many of the Webway Eldar are particularly odious, others lived in the Webway because they were trans-eldarists who the more conservative Eldar who lived in real space disapproved of. Even the murder-rape cults of the now Crone Worlds apparently believed in the sanctity of the Eldar form, both physical and spiritual. In Pre-Fall terms, what we're trying to do with our souls is what many of the Webway Eldar were exiled from real space for messing around with. In this pre-pain/soul eating era we may have natural allies amongst those trans-eldarists, as without the drive to cruelty that needing to eat suffering encourages they're probably much more interested in their attempts to transcend the limitations of Eldar nature than petty cruelty or such distractions.
And the people currently dominant in the Webway cities in this pre-Vect era seem not to be the Wych Cults or the more gruesome Haemunculi Covens or similar. It's the decadent pre-Fall nobility who sponsored those cults for their amusement, in competition with the Solar Cults, who are just bizarre in their own way, but not in ways Craftworld Eldar would probably care about.
And we may want share our soul modification process even with unpleasant examples of Webway Eldar mobility because even if we hate them they're probably less of a hassle if they have no driving reason why they have to enter real space rather than stay in the Webway and play their own petty games with each other, and because strengthening them against their even worse peers produces a lesser evil.