Judging from episode 24...
When Senketsu transforms into Senketsu Kisaragi after absorbing everybody else's life fibers, we witness his right eye opening rather than becoming uncovered (gif). This suggests that Senketsu was, initially, "blind" in his right eye before receiving enough life fibers to fix that, or something, and hence, that the eyepatch-like element on Senketsu's right is probably in fact just Senketsu's eye scarred shut.
It's not clear to me at this point how this relates to the notion that Senketsu is modeled after Matoi Isshin, given that Isshin wore an eyepatch over his right eye, but was probably not blind in that eye (judging from his face when he, as Souichirou, got out of the bodybag - screencap), unless whatever he did to change his appearance (plastic surgery perhaps?) blinded him.