The Gemara asks, just as Milla overides Shabbos (based on a Gezeira Shava), likewise Tzitzis and Tefillin should have the same ability. Perhaps this concept applies only to an actual Mitzvah like Milla, in contrast to Tzitzis and Tefillin which are merely preparations for a Mitzvah?
Abaye says we cannot derive Milla of a Katan Shelo Bizmano from the Ktan Bizmano; how is this compatible with Tosfos (131a D”H Veshavin) that it is the same actual Milla whether performed on the eighth day or beyond?
Tosfos earlier derived what they wrote from the gemorah that says we cant learn mila from the above mitzvos since if they are עבר זמנם their mitzva is batel’ not like mila. from here tosfos learns that mila is the same mitzva later too. but everyone agrees that mila in its time should not be pushed off as we would do to mila shelo bzmano since theit is a specific obligation to do it in its time. so even if you see that mila bzmana overides shabbos that dosent give us the license to do so with mila shelo bzmano. meaning that when regard to learning from other mitzvos to mila we say mila is not like them since its not over afterwards, so its different and cant be learnt out. but in regard to overiding shabbos there is surely a differnce between mila bzmano that when pushed off it will lose that importance.
To the first question, if the Pasuk would be telling us through a Gezeira Shava that Tefillin and Tzitzis are Doche Shabbos, even the Rabanan would have to agree that in these cases even Machshirei Mitzva will be Doche Shabbos since the Mitzva itself does not necessitate Chilul Shabbos. This is what we said earlier by the Lulav.
Another approach is that Rashi learned earlier that we are going by the Shita that Tzitzis is a Chiyuv on the clothing even while it is not being worn. Perhaps the Chachamim would agree by the last knot, which would be a Kiyum Mitzva itself, that it is Doche. Or even putting on the Tzitzis to begin with would be considered doing the Mitzva.
The same can be said for Tefillin. If we hold that the Keshira is not for every day and it is a Kesher Shel Kayama, then we are talking about the first time you put on a pair of Tefillin. And, according to the Shita that you make the Kesher every day — and that won’t be Chilul Shabbos since it isn’t a Kesher Shel Kayama — when the Gemara said what about Tefillin, perhaps it doesn’t mean Doche Shabbos; it means that we should be Mechuyav to wear Tefillin on Shabbos.
Also, perhaps Tzitzis and Tefillin are not considered Machshirei Mitzva. They are the Mitzva itself. Making Tefillin, and perhaps building a Succa, is preparing the Mitzva itself, unlike bringing a knife to be able to perform Mila. The Gemara earlier brought Tzitzis to show that Rebbi Eliezer doesn’t rule across the board that Machshirei Mitzva are Doche Shabbos, since by Tzitzis even the Mitzva itself is not Doche.