Conditonal...strategy

I am building an app where the markup is dependent on some PHP conditionals(the markup changes regarding the user that is logged in).

And from there js code must also reflect that fact…and the way to do it is this:
I just look the markup being present… (with JS code) and then act accordingly.

I just wanted to hear how do you judge the above strategy…for modifying JS code according to user logged in.

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