There are two separate questions here that are easy to conflate: (1) what color identity does a Phyrexian mana symbol contribute, and (2) does paying the Phyrexian life alternative produce colored mana? The answers differ, and both matter in Commander.
For color identity, Commander Rule 903.4 and CR 202.2c are the relevant rules. CR 202.2c states that a card's color identity includes the colors of any mana symbols in that card's rules text, including Phyrexian mana symbols. So a card like Gitaxian Probe with {U/P} has blue in its color identity, even though you can pay for it with 2 life. You cannot include it in a non-blue Commander deck.
For paying the cost, CR 107.4f specifies that when you pay a Phyrexian mana cost using the life option (paying 2 life instead of the colored mana), you are not actually producing or spending any colored mana — you are simply paying 2 life as an alternative. The mana requirement is bypassed entirely, not paid with mana at all.
A concrete example: Birthing Pod costs {3}{G/P}. Its color identity is green (the {G/P} symbol contributes green per CR 202.2c), so it can only go in green Commander decks. However, once you are playing it legally, you may pay its cost as {3} + 2 life rather than {3}{G}, and that life payment is not colored mana.
In summary: Phyrexian mana symbols do contribute their color to a card's color identity (restricting deck inclusion), but paying the Phyrexian alternative does not involve spending colored mana during gameplay.
Unofficial fan resource — not affiliated with or endorsed by Wizards of the Coast. Answers are AI-generated estimates grounded in the Comprehensive Rules and are not a substitute for an official judge. Verify anything match-critical.