Esoteric K-03X Runin RCA & XLR Outputs Separately?

Yes, definitely. You should break-in the XLR output circuitry using the same combination of upsampling and filters (or none to your example) to ensure the XLR circuitry has the same amount of time on it as the single-ended you wish to A/B. Esoteric gear sounds its best (IMHO) with its fully balanced circuitry in use; the break-in is vital to hearing this unit at its best. Also, no-up/no-filter may not be the best you can do with this unit. See many comments on other threads by many of us who own the upper Eso units (P/D and K); I think you'll find that after you break-in the unit with XLR, you'll also want to check out S_DLY2+176 upsampling and several other combinations.

I am finding that there is some glare and harshness listening with the XLR cable.

If by any chance you have performed the comparison with the RCA and the XLR cables both connected at the same time, I would re-do it with only one of the two pairs of cables connected at a time. While I suspect that in this particular unit the RCA and XLR outputs are driven from separate and independent output stages (which is often not the case with lesser designs), it is still conceivable that things like ground loop effects could occur with both cables connected simultaneously that could affect the sonics of whichever is being listened to.

Also, of course, be sure that the equipment returns to a full state of warmup after being turned off when the cables are changed.

Finally, keep in mind that the comparison you are making involves not only differences between the cables, but also differences between the balanced and unbalanced receiver circuits in the preamp or other component the K-03X is driving, and between the balanced and unbalanced driver circuits in the K-03X.

Regards,
-- Al

My Esoteric KO3x is fully broken in. i started with RCAs and moved to a higher XLRs and i am not going back

The XLR is the way to go.