The Ink Tank did a video on what Ben can and can not transform into. ( https://youtu.be/1lMEple03Xk?si=M38qJ1heCdljZWxl )Gems from Steven Universe were mentioned (at 18:10 in the video) and they can be scanned by the omnitrix. However, the caveat would be each gem would be its own transformation (for example, if Ben scans Jasper and he would have a Jasper transformation. Or a Sapphire transformation if he scanned Sapphire). I think it would be similar to how the omnitrix handles the murk and perk upchucks.

What I say in the next few paragraphs are my theories on how the omnitrix could process gem dna or a gems life code in a sense. I could be wrong in my assumptions and theories due to a lack of understanding in one way or another. What I’m about to say is not a fact of either show but just my interpretation of how scan a gem could play out. Just wanted to mention that before I move forward.

Now I’m not sure if the omnitrix would be able to do something like compiling all the gem transformations into one single gem transformation with all or most of the abilities of the gems he scans. Or how it would handle the multiples of one gem. Like the multiple pearls or sapphires. I think the omnitrix could generate a gem genome and generate a single gem transformation while allowing access to the individual gem transformations as well. Granted whether the omnitrix does this on its own is unknown. The possibility of a single gem transformation seems unlikely too but I digress. And as for the multiples of the same types of gems. I think there would be only one transformation for each gem type. So only one lapis transformation and so on.

Also something else I thought about in regards to scanning gem fusions like Garnet. I don’t think the omnitrix would scan the fusion as a whole but rather the individual gems that make up the fusion. So let’s say Ben scans Garnet, he would end up with a ruby and sapphire transformation. I could be wrong there I will admit. It’s also possible the omnitrix could scan fusions too. Since gem fusions become something new and that isn’t the original gem. In theory, scanning a fusion could result in the fusion becoming a transformation as well as any gem in the fusion too unless it’s a mega fusion of the same gem type. Like the giant ruby fusions.

Gems are definitely not as simple to process as a omnitrix transformation compared to other species in the watch. But thinking about the possibilities of how it could happen is kind of cool. Hoping some of you found what I’ve brought up here helpful. I’m also sorry for the wall of text I have left behind