I think the really important part is, as @llywela13 said:
They could have spent that time planning and coordinating, to ensure that everything tied together [...]. They just...chose not to.
It was a conscious choice the writers made. Matalas might not have been in the writers room for the entirety of the season 2 writing, but he was the show runner. They would have developed an overall concept for season 2 and season 3 before they sat down to work on the individual episodes, so he would have been aware of what was going to happen in season 2, at least in broad strokes, and he would have seen the season 2 scripts at the very least after they had been finalized.
So, major plot points like Agnes giving herself to the Borg Queen and petitioning to join the Federation 400 years later, Rios staying in the past, the return of Guinan, Q being the driving power behind the plot, ditching Soji and killing Elnor - all of that would have been established in advance. Hell, some of it even happens on the first few episodes that Matallas was still head writer for.
He might have expected Goldsman to write a better wrap-up for the season (like... an explanation for what the hell the cosmic force was that the new!Borg were trying to protect the Federation from. Or, you know, anyone in the present acknowledging that Rios and Agnes have suddenly disapeared???) But the existence of the galactic threat, for example, was established when Matalas was still working on season 2. So the decision not to tie it into season 3 in any way was his, in part if not in full. And it was a decision they made in advance. (He has said as much, iirc.)
Also: even though the writing happened concurrently, and the production on season 3 sets, costumes etc. would have happened while season 2 was still being filmed, the actual filming of season 3 started after season 2 was over. If, after seeing the scripts for the episodes that Goldsman et al. ended up with, Matalas had wanted to, say, put half a scene in episode 1 where he has someone say “We just received a hail from the USS Exposition near the Borg-protected rift and they’re saying everything is fine and the mystery will be resolved soon”, he could have added that into even an already existing script. Might have interrupted the flow a bit, but there could have been ways to do it without too much trouble.
Not making any reference to that was a conscious choice. AndI think you can say the same about most of the things left unresolved from season 2 (though I don’t feel like there were nearly as many plot points left in the air as there were after season 1, since most of season 2 was contained in the past with characters we never see again).
So while the concurrent writing certainly would have made an interconnected story over two season more difficult (or even two relatively self-contained stories that more thoroughly built on each other), it wasn’t remotely impossible. If they had wanted to, they could have done it, but they chose not to.
They have picked up little things here and there, like suddenly remembering Raffi’s familiy and history for more than a throwaway line about losing her sons and a longing glance at a glass of alcohol. But they’re not really building on Raffi’s character development from either season 1 or two. At least not so far (though, let’s be fair: we’ve only seen 2 episodes). So far, Raffi is in... exactly the same place she was in season 1? Pretty much? Making the exact same mistakes? Except now she no longer has Cris to hold her hand and help her through it, and apparently also no longer has Seven.
There is a reference to Picard’s synthetic body, but no indication why in season 1 he was adamant not to involve anyone from his old crew in the dangerous mission, and then in season 3 he immediately runs to Riker. Is it because he learned something in season 1? In season 2? Or is it just because we need to bring in the TNG alumns somehow?
Season 2 gave us the holos for a brief, terrible moment, season 3 isn’t even attempting to explain why Raffi is apparently all alone on La Sirena.
So, yeah, I don’t think the decision to ignore season 1 and 2 beyond superficial callbacks (so far) has much to do with tight schedules or concurrent writing. It was a choice, from the start, and a very deliberate one at that.
(All of this with the caveat that I only know what I have heard Matalas and Goldsman say in interviews and have gleaned about the Picard production process on twitter and through publicity. I might be mistaken about the timeline, or their concept of season 2 might have been more vague before Matalas moved on and he would have tied it in more if he’d had the chance. So grain of salt. But from everything I’ve seen, it doesn’t look like this was an external problem.)
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