It's not a better way that all xo parts use only one type of symbol although there is a work-around to deal with your unique requirements.
If you prefer see a only-2 pins-explicited schematics symbol for both of 2 logic-pins xo and more-than-2 logic pins xo, Just create different
symbol names for them. for one of symbols, you assign the global signal attribute on the symbol and you can associate with your more-than-2 logic pins xo.
If you only use integrated EE flow, you jut simply add "supply rename" attribute on the 2 pin symbol.
My chinese buddy,
see below's snapshot for supply rename usage.
1) create a symbol for 3 pin XO where you only explicitlly put 2 pin on the symbol and add attribute "supply rename" and assign a temp value, make it visible(it's useful to help deisgner get know there is another pin there)
2) create the PDB entry for 3 pin xo, just assign the temp value to the pin in supply assignment
3) put the symbol on schematics, change the temp value to current net name
the example, I just changed GND to DGND, now the pin1 of xo and the pin 3 of xo get connected.
I got your idea, Thanks, you helped me a lot.