Thomas is homegrown...he's from Atléti's youths. The others, like Gaitán, Augusto, Godín, Filipe Luis etc. have been in Europe a long time so to get eligibility (I confess I don't know quite how it works, but I do know Atléti has not been able to sign or bring in South American players many times because of the rule, same with Madrid)...Again, I don't think a very convincing solution to your argument is to point out how intelligently Atléti has worked around the rules. That's the whole point, if a similar level of manager to Simeone was working around them at Everton, they could certainly have had a rise like Atléti did. It's not like they've had anything even close to the level of Madrid or Barça in front of them in the league in the last 6-7 years.
The players you mention, Torres and Villa? Really? Reyes and Valerón of course did not participate in Simeone's success (I think Reyes coincided for a short period when Simeone arrived?) Like I said, your point is invalidated by the fact that an PL team can easily amass the same amount or more of foreign talent as Atléti has. The homegrown players of course don't have to be from Spain either. It's simply not as limiting a factor as you're making out.
The last line is again ignoring the 3 non-EU players rule, it doesn't really matter if they can get work permits easier, they don't have spots for those players unless they work the system quite well/are patient for players to achieve EU status.