Lets say I have 2 quartz crystals, one has 20ppm frequency tolerance specified in the datasheet and the other 50ppm.
It is not meant that way. Say you have a crystal with a X MHz printed on it. In actual operation, it may be X+/- y with a 99% probability. The y is the commonly meant tolerance. In a datasheet you may find three values: typical, max and min. Usually you will consider the typical value while designing some item.
Quartz crystals are less sensitive to temperature and the centre frequency will change with temp because of the temp effect on mechanical dimensions and elastic properties.
Far more important is the loading; that may affect the actual frequency much more than the tolerances or temp coeff.
You can tune a crystal (to a small extent only) by changing the loading. If the crystal is operated in a higher harmonic (say 2nd harmonic) these effects become less.
After both crystals go through the matching exercise at room temp, both crystal operates at their center frequency....
If you are trying to match the frequencies, obviously one of them (perhaps both) are not running at their centre frequency (because of the tolerances).
Near the centre frequency, the crystal may act like an inductor or a capacitor (depending on which side of the peak it is currently working).
Both parts may be considered equal for routine applications (but certainly not for critical applications).
Consider the crystals used in clock ICs.