Why not have rest hierarchy mean rest hierarchy, across the board? Here's what the "help" page for the Rest Hierarchy page says:
"From this page, you may set the player rest hierarchy the manager uses to determine playing time. This hierarchy is used in conjunction with the individual player AutoRest setting to decide who starts at what position and is also used during the game in blowout and injury/ejection situations. For instance, if Gomes is the LF in your starting lineup but his fatigue is below his AutoRest setting, then the #2 choice in the hierarchy would get the start instead. If he's not available, then the #3 guy gets the nod, etc. Before the regular season starts, users will only be able to change their hierarchies for Spring Training Squad rosters."
The implication is clear that the Rest Hierarchy determines who starts at a position if the starter needs to rest. There is nothing here to tell us that secondary positions are not considered; that if your backup second baseman is primarily a shortstop, then you're wasting your time - your 2b will play till he drops.
Seems to me they need to either fix Rest Hierarchy and secondary positions, so they work as implied; or that they change the wording about what Rest Hierarchy actually does.