Each exercise has its pros and cons. With each you train slightly different aspects, so it is good to alternate. You can also do a long series of short breath-holds with just a single breath in between them - in such way you'll be pretty hypercapnic for a long time without having to go deep into hypoxia. And in such case it matters little whether it is FRC or full lung. Though with FRC in such a series you reduce the comfort time considerably, so you spend most of the time in a struggle phase.
I totally agree with the point on short holds with almost zero recovery. In fact I always wondered why CO2 tables have to be so complex in terms of 'logistics' when the principle of what you are trying to achieve is relatively simple.
My answer to myself was always the fact that if the breathold is of a more realistic duration and profile of CO2 buildup it is more specific for real diving. This is the reason I am questioning CO2 tables with FRC holds because the moment you start changing another parameter, you can do simpler tables with shorter holds and shorter recoveries anyway.
Of course we also know that full lung CO2 tables are extremely dangerous and 1 in 3 people doing them regularly eventually dies from boredom. So the moral of the story is that if you don't want to die from boredom, do short FRC holds with short recoveries