Plan votes are always an option. The vote program accounts for it.
A is always the most score you can have in that area, with F being the least. But you also have additional capabilities to consider, so the letter score isn't the be-all and end-all.
When you tally the votes, if you're counting by plan then non-plan line votes are incompatible with the count and if you're counting by line then plans are just bundled line votes, easier to entre, maybe, but not distinct.
Which way you count actually changes what wins, and more importantly what is Able to win.
In complicated votes where the results interact such that certain options are desirable if certain others are also chosen and highly undesirable if those others are not, counting by plan allows for their inclusion because there's no risk of them being chosen Without Also having the necessary other option chosen. If the count is per line such options are usually non-options because of the risk of the other part of the vote going the wrong way.
As an example, we were very likely to end up with both aft torpedos and secondary phasers in the last vote regardless of what people Actually wanted, because anyone voting to Not include one risked not including the other Also winning, leaving the relevant arc unprotected, making them less inclined to do so, and even if they did take the risk, one person voting for phasers only and one person voting for torpedos only was identical in the count to one person voting for both and one person voting for no rear weapons at all.
Counting by plan, while not without its own issues, fixes that.
Simply voting for a plan when the votes are still counted by line does not.
