Arod was on the restricted list and still accumulated service time. Mike Minor spent 2 years on the Major League DL for the Braves and Royals and accumulated service time. Mike Minor has always been in the game. Kris Medlen is the player you are referring to here I think.
Usually if a player spends the entire season on the Major League DL he is usually in the game the following year.
If a player spends an entire season in the minors and never gets called up he loses his MLBPA status and isn't in the game the following year. Same goes for guys that retire and in some cases those who go overseas or head to Indy ball.
As for guys like Mustelier, Blackburn, and Zarraga they were September call ups, but never got into any games, but were in MLB 17 (same with Eddie Gamboa in MLB 16). This happens because they still turn in their MLBPA paperwork and become part of the union. People don't realize this, but players can join the MLBPA without pitching in a game or taking an official at bat.
Zarraga has 0.003 days of service.
SCEA actually messed up on Clayton Blackburn's service time. They have it at 0.004 and should be 0.007
Basically if you go to the minors (excluding a rehab assignment) and never come back up you are no longer part of the MLBPA. This is why you see some guys in each year and other's left out.