Created a thread about this a while ago... not sure if I submitted a bug report or not but I have to agree. All other companions can be geared up but the best poor SCORPIO can use right now are the 7 daily commendation armoring mods available on Illum and Belsavis.
The only other option that *may* be possible is to find a cybertech to RE higher grade armor mods until they learn the schematic. I'm hoping those would at least not be slot specific. However, I expect the mats to create them would make these items outrageously expensive for companion gear.
Sadly, this problem won't receive a lot of attention because there are only two classes that actually have useable droid companions: Imperial Agent & Trooper. No one brings their ship droid into battle and if they do its only until their healer companion is available.