ZAB Controller described a confused IFR departure flight from SRR to MMSD with some concern for terrain clearance; noting multiple flight plans and routes on file.

Narrative

I was working the R-Side with training in progress on the D. I was fairly busy. I learned about Aircraft X being cleared off the ground from SRR to ZZZZ climbing to 14;000 for the terrain. The route apparently originally cleared 'as filed' for was: SRR..ELP..CEN.UJ2.LTO.UJ9.LAP.UJ9.SJD..ZZZZ. The aircraft departed; I eventually RADAR identify him; then during his subsequent climb; I notice the aircraft was tracking much farther to the SW than direct to ELP; so I asked the pilot if was going direct ELP. The pilot says no and indicated he was going to RUTER intersection. At some point; the D-Side started investigating for flight plans and discovered a second flight plan for this aircraft in the system; also going to ZZZZ; but that apparently wasn't visible on the URET at the time they cleared the aircraft. The route the aircraft thought he was 'cleared as filed' for; and what he was performing was: SRR..RUTER.J13.BECON.UT13.CHX.UJ8.LMM.UJ51.SJD..ZZZZ. This is a fair departure from the route we thought we cleared them for. Upon inquiring the pilot further; I was able to obtain some information on how their company files flight plans. He stated to me that they go through a company and that they were responsible for the flight plans; and the pilots just go off what was faxed to them; or words to that effect. The pilot seemed awfully nonchalant about the whole thing; but that's another issue. In any case; I'm not entirely sure whether this is a flight plan issued through the FSS; with this company; or whether my D-Side actually looked to see if there were multiple flight plans in the machine. The trainer stated that there was only one SRR flight plan showing at the time; so they didn't feel it necessary to investigate for multiple flight plans; which is fair. A logic check in the system to disallow multiple flight plans for the same aircraft going to the same destination. An ability for FSS to remove proposed flight plans perhaps if a pilot updates their filed route or P-Time (if that doesn't already exist.)