1. Incorrect. For the emuMCC entry, it could be set up as payload= and have the same functionality. Only the sysnand CFW entry needed the fss0= syntax. The emuMMC CFW entry never did.
2. Except that there is no reason to disable them, especially with emuMMC CFW, and most people just wanted them to always load and everything to just work "out of the box". Thus fss0= style booting is best off unused most of the time, and absolutely should not be the default setting.
3. True, except when it is false, which it is for a certain piece of very important software that implements CSE when it detects Haruko's patches.ini. Again, people do not care about ideological about why this or that doesn't work or why they shouldn't be using that piece of software. With "payload=" syntax everything works, which (unfairly) but nonetheless does mean that "fss0=" style booting is needlessly complicated for people.
4. Atmosphere doesn't support fss0= style booting, only Hekate does which is why it is a hack, because Atmosphere does not natively support it. The part where hekate needs to get updated to use that "fss0=" syntax (but not for payload= syntax) is a litmus test for why "fss0=" style booting a hack. There is nothing wrong with it being a hack in and of itself, but it is a hack: an way of obtaining functionality that the software program was never intended to have.
See #1.
It is a con because it does not need to be used for that boot entry. payload= syntax would not change the behavior of that boot entry and using fss0= for the "CFW EMUMMC" boot entry needlessly complicates loading of patches for that boot entry.
That boot entry is also the one that everyone was basically always trying to use so it was the de-facto "default" boot entry. Team Atlas had no technical need to break things by including fss0= style booting in that boot entry and yet they did so anyway.
I do agree with you that Team Atlas did a lot of positive things for the scene, especially for new users, but using that "fss0=" style booting instead of "payload=" for that boot entry did a lot of harm. In terms of how the technology works, the scene will benefit from being united now compared to before because the principle entity that supported that technologically inferior way to boot atmosphere in an emuMMC CFW configuration (primary one for many people) will be dropping its support for it.
Hopefully that will lesson the need for 2 different sets of patches needing to be maintained going forward.