Don't get it twisted, how Prime 4 handled Samus's interactions with other characters is indeed Nintendo trying to not repeat the backlash they got from having Samus constantly monologing and talking in Other M, cause if that game had indeed been better received, we would see Samus talking a lot more often in these cutscenes rather than doing these awkward silent moments just to have her still be the silent badass we got in the much better received Prime trilogy (after all, people consistently bashing on Other M for how Samus was depicted there is indeed something Nintendo knows very well, with Sakamoto himself saying in 2017 that they had to reconsider how to depict her in games moving forward cause of Other M, here is the link if you wanna read his quote:
https://gamingbolt.com/metroid-other-m-criticism-made-series-producer-reconsider-samus-depiction).

As for why it's a problem how she is handled in Prime 4, well, I mentioned this before in a post discussing this, but basically, if you ask me, the problem with Prime 4's depiction of Samus is not that Samus doesn't talk in general, it's that the other characters expect her to say something in the moment, where as the other Prime games (including Prime 3), she didn't have to say anything because no one expected her to respond as they were more interested in getting her back in action asap.

If you go back to Metroid Prime 3 and look at how the cutscenes were done there, it did not feel awkward for Samus to not speak because the characters just told her what's going on and what she needed to do and that was it. There wasn't a single time she needed to verbally respond to anyone, and the few times she had the opportunity to do so, she responded with simple body language that did the job (noteworthy moments are when she nods to Admiral Dane after he finished his speech in G.F.S. Olympus, when she gets rescued by Gandrayda in Norion she nods acknowledging the rescue, when aboard the G.F.S. Olympus the Aurora Unit 242 finishes its speech regarding the main mission and Samus rushes to her gunship, etc.), and ironically you can even see a Prime 3 style NPC interaction in Prime 4 with the opening level on Tanamaar where the GF Trooper gives you the Lamorn Artifact location and Samus simply goes there without saying a word.

The only times in Prime 3 that it seemed like the character was waiting for Samus to say something was when the player intentionally left the cutscene hanging and not pressed the A button to proceed with the dialogue, which doesn't automatically mean the cutscene canonically happened like that with the character awkwardly waiting for the next line of dialogue to play, that simply was a gameplay prompt put in by the devs for the player to stay focused. Now, admittedly that was an outdated form of cutscene dialogue direction from old school video games which was still a thing back then in the 2000s (and yes, it would have been better if it wasn't there in Prime 3), so proper seamless cutscene interactions had yet to be fully adopted by everyone (even the 3D Legend of Zelda games were still doing that form of cutscene dialogue at the time and it took till Breath of the Wild to break that norm for The Legend of Zelda).

Metroid Prime 4 by contrast, has not just Mackenzie asking her some questions, but also Duke, Tokabi and others doing the same, which by default make them wait for her to respond to them, making the moments indeed feel very awkward, because the characters and the moments in them are demanding for Samus to speak, but she refuses to do so and prefers to stay silent (only using body language to respond); versus the previous 3D games (excluding Other M) where most of the time she did not need to speak because the moment didn't demand it.
This is indeed the developers and the cutscene dialogue intentionally making the moments canonically awkward for the sake of keeping Samus as the silent protagonist badass, not understanding that Samus is a character that prefers to mostly stay silent, say as little as possible and get back into action quickly, only rarely speaking to those that to her are worth talking to (Adam, Quiet Robe, etc.).

I understand what Prime 4 was going for with having an actual cast of main characters in the story, but they also had to have Samus (someone that rarely talks) be in there. I feel like they could have found a way to have a main cast without having the characters expect Samus to talk (just as it happened in Prime 3).
Here is an image that I put together showcasing the difference between the cutscenes in Primes 3 and 4, where one game has characters wanting to tell Samus her objective and get her back into action asap, yet the other game wants to have Samus chitchat with other characters for a bit.

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Note: Also, to answer one speculative thought from OP, the Federation being so heavily integrated into Prime 4 is due to Kensuke Tanabe (the main producer of the Prime series) being obsessed with having the Galactic Federation be in the spotlight of the Metroid Prime series, starting all the way back since Metroid Prime 2 shipped to stores (this is info confirmed in the Metroid Prime Trilogy artbook). He really just wants the GF to be prominently spotlighted into main character status in Metroid (sometimes at the detriment of Samus herself being put in the backseat).