Similarly, any end game and top flight raiders who worth their salt should know where they would suffer a loss of DPS. For example, MNKs don't need a parser to tell them that downtimes and dropping GL3 would screw them, and a BLM who knows their shits would know how to control their UI/AF so that they don't start the next part in a crappy state and suffer a loss in DPS. These people knows where they would drop their DPS, but would want to know how much.
So we are still back to a culled (downtime included) parse because we want to know what is on the table. We want to see the whole picture, as a fight itself. Because you want to see how each person, or even each job, can bring to the table throughout the whole of the fight. Let us use an extreme example - say maybe FCoB will have a turn where there are short 3 phases at first, maybe lasting 1mins each and the final phase just drags until the boss is down. However, the rDPS demanded from this fight is so high like how T8 started to be, your grp decided to go solo tank with 5DPS. Now, which DPS job shall your off tank change to?
If you judge by unculled (downtime not factored) then high burst DPS like BRD would likely to have some inflated number to fool your judgement if you believe it blindly. However, we know that jobs like MNK would build up DPS overtime but if you see the fight as unculled (downtime not factored) then the first 3 phases would penalize MNK already. So is bringing in MNK better or BRD better? You need to see the MERGED parse to be able to tell which job brings the most to the table for the entire length of the fight.
Inflated numbers from the unculled (downtime not factored) also gives a wrong feeling for fights with downtimes, and at the same time, a hard enrage. T9 for example. You hit the hard enrage for "some reason" and then you look at the parser and say, everyone seems to be doing 300DPS and why the hell are we hitting hard enrage? That's because the 300DPS marker is a culled (downtime included) marker for the whole T9 duration with downtime factored. Which means that you need to push harder than 300 during phases where you can engage the enemy, and don't be too happy when you see 300DPS for an unculled (downtime not factored).
It is also like, hey I am doing 350++ DPS during phase 1 part 1 but why are we getting 5 or even 6 meteor instead of 4? That's because your downtime timer is at a default 6 or below and doesn't take into account of the downtime during the dives.
There is a reason why people at the top and crunching the numbers stick by culled (downtime included) parses.