The token created by Will of the Temur’s first mode copies exactly what was printed on the original permanent and nothing else, with the listed exceptions (unless that permanent is copying something else or is a token; see below). It doesn’t copy whether that permanent is tapped or untapped, whether it has any counters on it or Auras and Equipment attached to it, or any non-copy effects that have changed its power, toughness, types, color, or so on.

If the copied permanent is a token, the token that’s created copies the original characteristics of that token as stated by the effect that created the token, with the listed exceptions.

If the copied permanent is copying something else, then the token enters as whatever that permanent copied, with the listed exceptions.

Any enters abilities of the copied permanent will trigger when the token enters. Any “as [this permanent] enters” or “[this permanent] enters with” abilities of the copied permanent will also work.

If a permanent has {X} in its mana cost, X is 0 for the purpose of determining its mana value.

The commander you control doesn’t have to be your commander.

Once you’ve announced that you’re casting this spell, players can’t take any actions until you’ve finished doing so. Notably, opponents can’t try to remove your commander to change how many modes you may choose.

Whether or not you control a commander is determined only once, as you choose the modes for this spell. If you somehow lose control of that commander before you finish casting the spell (perhaps because you sacrifice it to activate a mana ability), it won’t change the number of modes chosen.