Flowey was made from the first golden flower that grew in the Underground and was infused with Asriel’s dust.
All the other golden flowers descended from that one but I guess monster essence magic does not carry over genetically.
Yeah, she tried lots of flowers, but only the first one changed noticeably.
Personally I think a flower from the surface would have to be pretty dang DETERMINED to bloom in the Underground, especially outside of Asgore’s garden, so I can’t help wondering if it was just a change Alphys wouldn’t have noticed since she isn’t a plant person…