It depends on the context. In-game, as long as it is acceptable within role-play and the written rules then it doesn't matter.
If a faction leader is away then they may divert their abilities and responsibilities to their number two in such a way that they will temporarily transfer complete control over the faction. An example of this could be in Star Trek whence the Captain goes on an away mission, they will designate a temporary ship Captain (or if the Captain cannot personally do so, the next lowest rank that is available will by default assume captaincy) that will inherit the rank until such a time that the Captain returns to the Bridge. All subordinates will respond to them as if they are a Captain. In the event that the Captain does not return, High Command would install a replacement or promote an existing officer to the position of Captain.
I'd have thought that so far as the Admin are concerned, if they have a matter that needs the attention of a faction leader then they would likely allow the number two to handle the matter if they trust that they are capable of doing so. It's unlikely though that there is any kind of official stance.
as second in command, you get to play with the toys when the boss is away.
in game, this is a given.
in forum, if the boss is away for short periods, just say "big man take holiday he come back soon".
but if he is away for long periods, best get him to post that you're in command until his return.
the rights you have as 2i/c when the boss is around is generally upto yr boss. i think that 2i/c's can FR5 someone and can grant access to ships/weapons, even when the boss is around, but thats about all i think