This is how it is currently working, not sure if it's a bug or intentional. The 'Righteous' gear that is given to you by the season pass, counts as a 'different' gear piece to the same items which drop from things like the Sundial or the Obelisks. So despite having the exact same name, because the game treats them as being different, it makes you use an Upgrade Module instead of Glimmer if you try to infuse a Sundial-dropped Righteous piece into one given by the season pass.
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That's correct, I thought same. But the only other thing - I try to upgrade gear not from season. All gear from season can be up with other "Righteous" pieces, obtained with Sundial or Obelisks or other activity. I cheked this. On the screenshot you see piece not from season rewards - it's piece from Obelisk (or pvp, I'm not sure). And all of my friends didn't even run into this problem. So, in my opinion, that work isn't correct. Maybe Bungie even doesn't know about this case.
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So if you level up your season pass, you get perks that can drop "extra" pieces of gear... those extra pieces are season pass items, even if they come from an activity that would be considered a non-season pass source.
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Unfortunately, the fact that I accidentally destroyed reward from this season pass (just a two pieces). I think this case should be thought out in advance. And all of season gear obtained from any activity should be work correct, when you try to up this.