PLL comensate issue

The compensation is basically the idea that it's compensating from the clock input to the clock destination. This clock is recovered from a transceiver, and so the whole delay from the transceiver to the PLL is not compensated. Now, in your case that makes perfect sense and you really don't care. The warning is more for the person who brings the clock in on a pin that doesn't directly feed the PLL and thinks they'll get timing as if it were on a dedicated clock input that feeds the PLL. (For example, you get good Tco times. But in your case Tcos don't make sense by themself, since there is no true reference for the clock). Basically you can ignore this warning.