Tosafos (d.h. shene'emar) asks why does the gemara choose to cite the pasuk of lasheves to justify the importance for the half-eved half-ben chorin, to be able to procreate, rather than the more well known verse in the Torah of P'ru U'rvu? My understanding of Tosafos answer in the name of the R"I is that the mitzvah of p'ru u'rvu is really a ma'aseh mitzvah like any other where we have exemptions for o'nes. Therefore, citing the pasuk of p'ru u'rvu wouldn't justify forcing the master to free the eved since at the present time the half-free side of the eved is exempt as an o'nes because he is incapable of performing the mitzvah. But by citing the verse of לא תהו בראה לשבת יצרה the gemara is pointing to the root and purpose of the mitzvah of p'ru u'rvu. The pasuk of La'Sheves Yi'tzara illustrates that the purpose of p'ru u'rvu is to occupy the world and therefore we don't follow the regular system that we do by other mitzv0s, because even if he is exempt due to o'nes the world will remain empty. Although the gemara means to use the pasuk in the torah as p'ru u'rvu as the source, it chooses to quote an alternate pasuk that would justify why p'ru u'rvu should apply even in a circumstance where he is an o'nes.
This approach is very meduyak in the language of Tosafos where the entire focus is on the pasuk chosen by the gemara, rather than using language that indicates that p'ru u'rvu isn't at all applicable since he is an o'nes. Tosafos language implies that p'ru u'rvu is truly the source that compels us to force the master to free the eved, but we cite the pasuk that explains why p'ru u'rvu should apply even to a circumstance of o'nes.
Furthermore, this approach would compliment, rather than contradict the Turei Even in Rosh Hashana 29a who asks that since one who does a mitzvah when they are exempt doesn't fulfill their obligation, how can the gemara in yevamos say that if one had children as a goy an then converts his whole family he automatically fulfills the mitzvah - the mitzvah was done when he was patur so he should have to do it again? Turei Even answers that since the purpose of p'ru u'rvu is to populate the world, we disregard when the act of the mitzvah was done so long as the world is being popluated as a result of his actions. If we were to understand Tosafos simply that only sheves applies but not p'ru u'rvu, then the Tosafos would be holding that p'ru u'rvu is a standard mitzvah like any other where o'nes is exempt and the ma'aseh mitzvah should have to be done when he is obligated in the mitzvah. But since we are explaining that according to Tosafos the entire mitzvah of p'ru u'rvu is for the purpose of l'sheves yitzara - populating the world, Tosafos is essentially a support for the Turei Even's chiddush that the time of the ma'aseh mitzvah is not rellevant.
This also explains how in the very next Tosafos they are able to ask that the mitzvah of p'ru u'rvu should push off the issur of marrying a kadeish. How can Tosafos cite the mitzvah of p'ru u'rvu moments after saying that it doesn't apply here since he is o'nes. Clearly, Tosafos never meant to say that it doesn't apply here, rather just that we wouldn't realize that it does apply here if not for the fact that we quoted the verse of l'sheves.
As a side note, there is a famous discussion whether an o'nes is exempt or actually obligated but unable to perform. Tosafos here seems to support the former. Tosafos explains that since the half ben chorin is an o'nes in his obligation of p'ru u'rvu, we wouldn't force the master to free him. Tosafos supports this claim from the fact that we don't force masters to free all regular avadim to enable them to keep mitzvos. Now, if o'nes is actually obligated but unable to perform, how can Tosafos prove their case from a standard eved who isn't even obligated at all in the mitzvos. Perhaps we don't free regular avadim because they aren't obligated but we would free this half eved since his free side is obligated just that he is an o'nes. Clearly, Tosafos holds that o'nes and not being obligated is exactly the same and can prove o'nes from the case of a regular eved.