Faction members are not aware of faction ownerships in barter
Vanilla: faction members react when you try to sell them something stolen that belongs to their faction, the same way they do with items that belong to them personally.
#2 Updated by rot tor about 2 months ago
I think I already commented on how illogical the reaction could be somewhere else, but MCP even disabled it as a default bug fix:
Certain storage containers are faction-owned, with the items inside belonging to the faction. These are not items for sale (as those must be owned by the merchant), but merchants will still consider all items of that type stolen. This could result in merchants recognizing and seizing any type of item taken from a distant town, which is not particularly believable. With this option, merchants buy items stolen from faction containers without issue. The act of taking items out of faction containers will still get you in trouble, if you are seen.