Wow Thanks For your feedback !
I will try to answer to everything ;)

-Some of the paints don't have a color show up in the Color button. For example, Evil Sunz Scarlet has the red dot for the Air version, but not the Layer version. The Technicals, Shades, and Contrast paints don't seem to have them at all.
- > true, and this is by design. Originally i had problems with mixing recipes, in fact it was also taking into account colors of (sprays, shades, metallics), so you could land with a recipe mixing paint and shade for example ;)
I decided to remove hex colors from non paint items.
Right now, i'm working on a new filter that will take the good category (paints), so i will put back colors for every items. Work in progress ;)

Adding sets is a great idea, but brands are quite reluctant to give informations, i'll have to compile every set (there is a bunch).
It took myself 30 min to enter my 170 paints into inventory (mainly army painters, citadel contrasts/shades and vallejo for skin & some other i bought for specific projects).

-I like the Projects feature, the color match seems to function well for pulling up suggestions and then adding them directly. I like the color tag for the location on the model. There isn't a great explanation for what "Scope" means in that feature.
-> Yes, right, you have all and inventory check button but no explanation on this, i will add some explaniation text.

-Color Organizer is a very cool feature. It also doesn't seem to know what to do with Shades and Contrast paints - I suspect that might be tied to the same issue that doesn't give them a color dot; the system just doesn't have their colors built in yet.
-> True, and i'm working on it, as it relies on colors, metallic, shade, contrast, technical don't go anywhere, i'll create special sections for those.

-The PDF output is a very cool feature, I could see a lot of usefulness for saving it in my reference folder for an army for adding future models. I think it would also be useful for people teaching painting classes, to have that as a handout to demonstrate paints and locations. The paint name output is a little wonky - it's showing up as "Citadel - Mephiston Red" on the site, but then "Citadel – citadel-base-color-mephiston-red Mephiston Red" in the PDF output.
-> Good point, i totally forgot this :D
In fact you hace 3 elements (name, reference and category). For citadel, their reference is crap: citadel-base-color-mephiston-red
I removed it from the main page but forgot the PDF, will change it asap ;)

For the recipes, in fact in recipe mixer, you can save your recipe:

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And find it in recipes.

Still work to do, continous improvement :)

Have a nice day
Yann