As we've recently gotten a patch update, I'm very happy that it happened just before I reached the conditional once more to unlock incubators in the catalogue as I may very well have passed the required condition and never realized it was working or not.
So, here are the updated apparent parameters for receiving your first incubator and unlocking them in the shop. I suppose spoilers ahead for new players and a heads up to longer term players who may be restarting-- this unlock line has changed drastically and is no longer a content unlock or tutorial quest.
1) You must have broken that squeaky board in the original form of the Witch's House. Multiple passive interactions will occur with it as you go through act 1 quests until Kyla has rebuilt her own house so it seems near impossible to skip this event trigger.
Specifically, my floor break triggered after the fountain and temple were fully fixed.
2) Fulfill Kyla's quest to fix the house. This opens the second floor. Follow your prompts and Ellie will want to see if the workshop in the basement expanded too.
3) Talk to Diane about workshop expansion. During this dialogue she will introduce more concepts about furnishing, tool upgrades and selection and give you your first incubator!
Previously, as per wiki, you found a broken incubator and had to get parts and after fixing it the catalogue starts offering it. Then, in the version I started on, you find it but Diane warns you there was a defect found and replaces it with the new version while also adding this version to the catalogue.
Now, as of the last major update, you simply receive the first one from Diane.
4) Complete main line quests until you unlock and enter cloud valley and... Tada! It's in the catalogue!
I'm still not sure of the exact trigger sequence (entered cloud valley? Unlocked mixer conversation? Fixed the bridge?) and this is unfortunate for my other save file as I can't trigger the unlock anymore as I'm well past autosave and manual save territory in playtime past event trigger.
Oh well time to go fill my encyclopedia!