I don't see the problem with regarding a trilogy as separate films. They are separate films, and sometimes one is better than another. The only issue is that it takes up space on your list if you intend to vote for more than one part, I suppose. But splitting didn't harm Lord of the Rings in the Millennium countdown, and at least with it split nobody could say 'it's only number one because you combined the three films'.
And that's one of issues I have. I want all
Three Colours films to do really well, but there are at least fifty 90's films that can make my top 25, I really want to give every film a chance.
Besides, if we enter them as separate films, they could easily get lost in the shuffle. Some very few will vote for Blue, some for White, a lot for Red. It just makes the chances of any film getting a decent position or even actually making the top 25 rather slim.
I think some trilogies can be viewed as separate entities, but
Three Colours is an exception. Each of the three colours represent a colour of the French flag, this is thematically important when looking at all the films as a whole. If you were to split them up individually then it somewhat loses that thematic relevance, I think.
I think i'll have to watch every single 90's film that made it to my Top 100 (though that list would change drastically today) and some more I admire a lot. I'll watch at least one a week until the week before the deadline. Should be exciting.