Once you've announced that you're casting a 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.

Even though the card is named after a specific character, controlling any commander will satisfy its condition.

There's no extra bonus if you control more than one commander.

Once you've chosen both modes for the spell, it doesn't matter whether you continue to control a commander. This is true even if you somehow no longer control a commander as you finish casting the spell.

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

"Protection from each color" is shorthand for protection from white, from blue, from black, from red, and from green. Colorless is not a color.