A lot of people seem to be misunderstanding what the problem is. It has nothing to do with the Master and everything to do with the ranks below.
Fictional FC organisational ranks:
1 Master
2 Treasurer - only one person other than master who can withdraw gil and items from the chest, let's say they're a lifelong trusted and trustworthy friend of the Master, they also use an authenticator and never go to dangerous sites, etc
3 General leaders - these guys can promote people from the social rank into something more specific, indicating what that person does for the FC, they may also lead events, etc
4 Crafters and gatherers - who you go to first to ask for things to be produced/melded/gathered
5 Combatants - These would be the professional raiders and FATE grinders and chocobo trainers and everything else involving whacking/zapping/band-aiding something/someone with other members of the FC
6 Social - the first rank someone goes into when they join, before they become well known for one of the above roles, also good for the casual jack of all trades or those who don't participate much
Say a bigger FC absorbs a smaller FC and the leader of the smaller FC is given the authority to bring in and promote their members to the appropriate gatherer/crafter/combatant/social rank as they're the ones who should know what their members do. Presumably the company chest is still safe because only 2 people have been given access to that: rank 1 and 2, Master and Treasurer, both above the rank of the promoters.
The leader of the smaller FC can promote another member to a higher (but still non-Master) position than the promoter is currently in, meaning they can make their entire FC (other than themselves) Treasurers without permission and rob the bigger FC blind.
That is the problem. It has NOTHING to do with the Master rank and everything to do with every other rank.