Yes the alert tones are a little funky but they do nothing on the system. The tones open up VHF pagers carried by emergency responders. The voice is ok but understand it is a VHF bridged over repeater to a TAC.
Tones sent over P25 will sound wierd. The P25 vocoder (as are most speech centric vocoders) is designed to digitize human voice. Paging tones are continues tones of a set frequency, very unlike human speech.
And you are right, it doesn't matter since they aren't needed on the trunked system. If they wanted, they could use the console to send the tones to VHF only, and the voice part of the page to both VHF and the P25 system. This is what Colonie does - the paging tones never appear on the trunked system.