Whether the resulting flowers is hybrid or not depends on the genes of the parents. I don't think you'd get normal red roses, for example, if you tried to breed hybrids using an orange rose and a non-hybrid white rose because only one of them has a red gene. If you used a red and a purple, you could get a normal red rose because the purple can have at least one red gene.
The normal ones show up in the same spots as hybrids, which is next to the parents in some way. There is no real way of telling them apart, unfortunately, so if you want to be extra safe, I'd use a combination like orange and non-hybrid white. You should also make notes of where you laid out the parent flowers, so you know which ones are their offspring, and to put them somewhere your villagers won't go (if your villagers go to your beaches, you can dig holes around the flowers, I think).
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It's a flower that looks red but has different genes instead of only red genes. They're used for breeding some hybrids like blue roses or purple pansies.