For some reason, having Tenebris Prime active locks the entire Storage Optimizer research chain behind the bioinfusor tech, making the whole thing post-Aquilo. I doubt this is intended behaviour, so it might be worth looking into why it automatically places it there

Thanks for the report, you were right, that wasn't intended. Tenebris Prime adds a glowing copy of every belt with the same speed, unlocked by bioinfusor. My mod builds one tier per belt and sorted belts of equal speed alphabetically, so bioluminescent-transport-belt became tier 1 and the whole chain ended up behind bioinfusor.
Fixed in 0.4.1: for each belt speed, the tier chain now uses the belt that is available first. The glowing belts still get their own optimizer tiers, but as optional side variants crafted from the normal tier, so nothing in existing saves is removed. I tested it with Tenebris Prime 1.3.10, the last version for Factorio 2.0. If you play on 2.1 and something still looks off, let me know.

The Tenebris issue is now wonderfully resolved, thanks for that, good work.
Getting various different mods that interact with belts to play nice together isn't an easy thing. I did some extra testing, and if there's several mods that add belts, they can lock Storage Optimizer's research paths behind eachother in unexpected ways. The example I found in testing was an interaction caused by having both Planetaris: Hyarion and Ultimate Belts Space Age active, where most Storage Optimizer upgrades based on the latter would be locked behind the belt research of the former, presumably on account of Hyarion's belts being slower due to different balancing philosophies. This leads to a situation in which I can't research the Storage Optimizer for belt tiers I have unlocked via UBSA until I progress significantly further in the game than the point at which I get said belts

Thanks for the detailed testing, that was a great find. The hyper belt actually comes from Planetaris: Arig (Hyarion moves its research), and the same problem also hit Ultimate Belts with plain Space Age, where its belts waited for the turbo belt. Fixed in 0.4.2: tiers no longer form one chain sorted by speed. Each tier is now crafted from the fastest slower tier you are guaranteed to have first, meaning its belt is an ingredient or its technology is a prerequisite. With your mods, the Ultimate Belts tiers branch off the express tier and the hyper tier follows turbo. Tested with Arig 1.1.46 + Hyarion 1.3.22 + UBSA 1.3.0 on Factorio 2.0. Existing saves keep everything.

Splendid. Good work staying on top of it, I'll be sure to inform you if anything else crops up. Thanks, and best of luck!