So implying it's a reference to something can get you in trouble when it's Xeno related but Sakurai can imply some costumes are based on Star Wars and Gundam and hint at Kinnikuman's Spring Man. This makes less than zero sense, especially as nobody's ever gotten in trouble in the gaming industry for making references to other media, other games or even namedropping Satoru Iwata. The Xeno series isn't special enough to suddenly create legal issues you know.
The tongue-in-cheek reference to mass produced Zakus with Green Samus being 'Mass Produced Samus' was done with the very first title, when Smash wasn't the juggernaut series it is now and a time when Japanese companies weren't as gung-ho with their IP Protections..I mean, Smash 64 had the Beam Saber even make the same sound as Light Sabers in Japan. I don't recall Sakurai ever mentioning an alt was a reference to Star Wars though..
The Kinnikuman Spring Man reference was done during a live stream and isn't present in the game itself, so yes, its fine.
Yes, but they've never been direct about it by confirming that the reference was to another series, regardless of how obvious it might have been, especially in Japanese games, even if Sega used to do it with Spider-Man & Batman as bosses in Shinobi..going so far as to license Spider-Man in the West to keep half of the boss intact, and even originally having one name Mari-Oh in another game that was a deadringer for Mario before being redesigned to not get into legal trouble, though keeping the Mario reference by having the boss shrink after enough hits similar to Super Mario shrinking to Mario after being hit.
Xenogears is owned by Square-Enix and they are very protective of their IPs, regardless of how 'special' it may or not be..I mean, the main character even got a Bring Arts figure not long ago, so they clearly still value it as a series. Xenosaga would be a little easier to get the okay for, considering Namco is developing Smash Ultimate with Sakurai and both KOS-MOS and T-elos being in Xenoblade 2, but they could also have felt the hassle wasn't worth it. All the same, it doesn't matter if an IP is being actively used or considered 'special', the IP Holder still has the option to defend their Copyright, regardless of how trivial the particular situation may seem..so its often better to play it safe than sorry.
There's a reason so many items in Smash Bros, such as the Proximity Mine, Beam Saber, and more were redesigned.
All I'm saying is that there's a possible reason Sakurai didn't outright call Pyra/Mythra's Alt 5 'Weltall', Alt 6 'Xenogears', Alt 8 'Zohar'..though not calling Pyra's Alt 7 'Monado' is funny if it isn't a reference to the Monado's colour scheme..though its possibly due to not having a colour scheme reference for Mythra in that alt and just making a complimentary one.
Honestly though, referencing Xenogears and Xenosaga without directly stating the reference is pretty inline with how Xenoblade does things, considering the Conduit is just straight up the Zohar, even called the Zohar in the game's code, which is a plot relevant artifact in both Xenogears and Xenosaga, albeit with a somewhat different design in each appearance..though the Conduit is the closest to the Xenosaga Zohar, and then Pyra's stasis tube is very similar to a similar thing in Xenogears.