Theoretically the PCs, behind the scenes, need to explain just where the items they confiscate come from and just what their significance is to the case at hand. "Oh yeah, we found this on Dead Suspect."
The Guide doesn't say that. If one of the PC's dies, is it expected that his worldly possessions pass to ownership of the RHC, or might the PC have a will leaving those possessions to friends or family? I would expect the RHC is primarily funded by the Risurian treasury, and not by confiscating whatever it lays its hands on.
The PCs are lying through their teeth to their superiors. Call for Bluff checks. And if the PCs don't have their story straight, send the DCs through the roof.
Assuming the RHC needs equipment, presumably it is purchased from somewhere. Why would it be restricted to craftsmen or spellcasters other than RHC members? If the RHC needs a supply of Long Swords, and an RHC member is able to produce some of that supply, why would he need to lie for his employer to purchase them.
Even so, maybe they get away with it once or twice. But eventually somebody's going to notice that shiny new items keep showing up at the RHC as "evidence" or "confiscated property." Or maybe there is a random audit of the evidence room, and something PCs turned in just happens to be selected. Either way, it won't be long before the RHC sets a couple diviners loose to figure out just what the provenance of these things is.
Again, this assumes the only items the RHC has are those held as evidence. Why? And why would they let the constables requisition that evidence, then take off for parts unknown on assignment, if it is needed as evidence?
This does add another wrinkle - should a character leave the RHC (on good terms - retiring or taking a position elsewhere) is he expected to return the equipment acquired through the RHC? If so, does he get the money back?
IOW, if the PCs abuse their position in this way, they should get caught, fined just enough to set their on-hand cash amount to the "right" level, and put on some kind of probation. Which still shouldn't cause a huge problem with the Adventure Path, because you can always set up the next adventure as the most awful case on the docket, given to the PCs as punishment for their transgression.
I don't see why one jumps to this being "abuse of their position".
ETA: You could also short-circuit the whole mess by simply saying the PCs have full-time jobs already, and severely curtail the amount of time they have "free" to make Craft checks, unless they want to go without sleep....
They certainly have limited time. No time? Then why even make Craft skills and Creation feats available? Pathfinder even added the ability to get a couple hours of work done on an adventuring day, presumably to ensure these feats, especially, have some utility. As a player and a GM, I think the players have the right to expect to use the feats and skills they select. If a given skill or feat will have no in game benefit due to the way I run my game, I will tell the PC's that. I won't, to use a Zeitgeist example, wait until the Sorceror picks "Overland Flight" as a spell, then chuckle as I point out its capped duration. I'll tell him that, due to the Zeitgeist setting's special rules, that spell is useless and he should choose something else. Similarly, if there will rarely or even be down time to craft, I will tell players not to waste their feats or skills on those abilities as they will not be useful in this game.
Using these as a "gotcha" strikes me as poor GM'ing, and poor sportsmanship in general.
In any case, why would any PC be assumed to be willing to lie to his RHC superiors and cheat the RHC and, by extension, the government of Risur? EVERY PC begins play with a strong loyalty to the nation. They have "
passed a background check and magical inquisition to prove his or her loyalty to Risur" - I don't think they can be Bluffing that loyalty. How would they suddenly become disloyal skimmers and liars immediately after joining up? [hmmm font changed when I copied from the Guide...] Assuming the PC's motivation is cheating the RHC seems, to me, to assume the players are horrible role players. The RHC has to get its gear from somewhere - to me, that is the reason they would pay full price for used PC equipment. They're not BUYING it to put in the evidence room, whether it originated with an item seized by the PC's and requisitioned back or somewhere else, are they?