Actually, the capacity for eye development is encoded at the root of the phylogenetic tree of life. Pax6 is a gene involved in eye development, for example. When you BLAST (blastp; default search parameters) the protein encoded by Pax6 (accession number: P63015) against the domain Prokaryota, you get significant hits (E-values < 1e-05). A PSI-BLAST search would almost certainly uncover hits with even greater significance. This suggests that eyes (and other major organs in Metazoa) were anticipated by the first genomes.
But with the ToE, we wouldn't expect a gene to come about from nothing. Its going to have to be a modification of a previous gene. Your evidence is consistent with the ToE so it doesn't suggest front-loading over it.
I have a hypothesis that gravity is caused by little invisible angels dancing on top of everything. If I let go of a ball, and it falls to floor, then that suggests that there are little invisible angels dancing on everything, right?
Arguing that the sub-optimal codes once did exist early in life’s history, but vanished once the optimal codes came on the scene (i.e., that they were outcompeted), looks awfully ad hoc.
Wait, why? Isn't that exactly what is expected to have happened?
I'm still wondering why you call that "ad hoc" and why you think it is.
Further, I don't see any reason or evidence to think that some ancient aliens seeded our planet*. What you've got is the idea that something like that happened, and then you're looking for evidence that would be consistent with that happening. You can do that all day, but if that same evidence is consistent with a better idea, then that idea's gonna stay on top until you overturn it. A better approach would be trying to prove that front-loading did NOT happen. What would you expect to find if there was no front-loading and can you find that?
*The only reason I can think of to introduce front-loading would be to leave room for introducing god into the equation. What other reason is there?