Allowing GMs to reserve seats at their tables is not something we will be implementing in the near future. There are many, many other things we would love to improve about our registration system that are higher on the priority list and, ultimately, that's not really the core thrust of events at Gen Con.
The convention is (very broadly) about organizing folks who don't necessarily know each other together to play games. Setting up a system to allow folks to run private or semi-private events would be nice in some specific cases, but drifts further away from that core mission and is not a high priority.
Until our approach changes, the policy stands: run your event as you submitted it. If you are planning on having 5 players seated at the table running games, do not submit an event for only 3 players.
Again, if you want to run a game for some people you know and some folks you don't, you can just recruit those players directly yourself (even here on the forums) and then just walk up to an event HQ onsite to ask for an open table, and then you would get exactly what you are requesting entirely within our stated policies.
"I guess I'll just be a bad person" is not a stance that ends well, in almost any circumstance. Please avoid the headache that will create for all of us.
Senior Event & Program Manager
Gen Con LLC