There are several aspects to consider.
1) Defense : Thurophoroi and Thorakitai have different defense characteristics against different kinds of attackers. Just check their descriptions.
This means a good defense would involve mixing them to get a more extensive defense against most kinds of attackers.
2) Offense : could be selected depending on the expected ennemy defense, taking advantage on the defender's weakness against some kinds of offense.
This is the same reason why you get different results on Persian positions depending on their contents. For instance, all horses have a ridiculously low defense value against infantry offense !
3) Grain consumption : higher kinds of units consume more grain but have a better power to consumption ratio. So a full cavalry army will eat less grain than an army worth the same power, but made out of other kinds of units.
In the end, you'll want to get as much horses and phalanx as possible for PvP and sacrifice infantry to Persians to get more cavalry and phalanx.
4) Cost (in resources) to damage ratio : when playing Persians, you now have two different strategies : either playing as many positons as you can to collect as any partial payouts as you can on the go (my method), or investing as many resources as you can to get the full payout as fast as you can (old method).
Everybody choses what suits them best, but if you're using the old method, you'll want to sacrifice the most expensive units. That's where being able to chose among more or less expensive units helps.
5) Simply what you get : you get 90% of your cavalry and phalanx through playing Persians rather than building them by yourself, and you get only those two kinds after level 40 or so anyway. In addition, you don't chose what you get, so just get them and be done with it.
In the end, since you're getting more and more phalanx and cavalry, and they're the kind offering the best power to consumption ratio, you'll logically want to stack these ones and sacrifice the junk (infantry).
So just pile up cavalry and phalanx, and don't care for the models you get. Just use them all when fighting, period. Why caring ? They come as they are anyway, and you never know before you finish off the Persian position.
I'm not asking questions nor philosophizing about what I can't control. What for anyway ? They're there, they can fight. All good.