Ok I'm going to point out a couple things here.
First off the DoT formulas are not right in v4.0 onwards. (this is easily proven by adding 1 sTP to any gear set and noticing it will minorly change your damage output - which makes no sense unless it changes your xHit build). Upto including v3.2 I had a factor called 'Effective Delay' which just modified your natural delay/haste/DA/TA/acc. into one factor with 100% accuracy. This worked pretty well, but for some multihit weapons it certainly wasn't ideal. Masa added a nice table to calculate probability for any given round in v4, but made the mistake of scaling TP to account of DA or accuracy instead of time. We'll looking at trying to do a full probability table, but the math is very intensive. Its been a good 10-12 years since I've taken statistics or probability and I don't have much free time to work on it, so its been slow going.
2nd: the tool is used for comparing setups in ideal circumstances, which really don't exist. The DoT portion can be tested agains Fortifications without Lag. (ie checking DA rates, average TP return, average TP started with on a ws etc..) Other parses you can compare more generic information such as your max/min for regular melee or crits. Obviously when there's pauses in battle, you get TP from getting hit, you get feather tickled the mob runs away because a mage pulled hate, etc. etc. the DoT piece won't match up at all. But that's irrelevant for comparing gear (most of the time at least, some situations the continuedness of the fighting is likely to make a logical decision as to why an answer might not make sense). Also comparing the data to a random parse isn't entirely valid just because gear swaps might not be consistent, debuffs and mob levels may not be consistent (although kparse can filter mob levels).
3rd: it clearly does not calculate ever niche circumstance correctly, I never figured out a good way to have the 15% AGI bonus of the Rogue Armlets+1 work (but you can easily do the math your self and add the bonus - then the sheet does the rest of the calculations). It attempts to do somethings though such as estimate Souleater damage based on your HP - although I'm pretty sure it assumes you are not cured.(I don't remember and I'm not sure if Masa changed it, I set it up well over a year ago). Buffs can be tweaked very easily if you have the world's luckiest COR you can just go to that page and change the attack modifier to the % needed for 11s.
As a melee paying attention and not being an idiot with adequate gear will often make up for getting uber gear+1. (engaging mobs quickly, not WSing @1%, riding recast timers).
I don't see a Butachi +1 in the default gear list, so I think you're talking about a different calculator.
Well yeah that's one of the main reasons I advised against using the calculator, lol. Besides, calculating DPS with entire sets is needlessly complicated and far too much work when it's way easier to just compare two items back to back and how they improve the gearset as a whole.
But why stop there, maybe people shouldn't use a parser either, just go out and whack a mob once and compare the 2 numbers.
Finally, its obviously the goal to make this as accurate as possible, but I would tend to think some changes (such as the ws delay) will make little difference for comparison sake because it will be equal between both, but when its easy enough to have a tool do it all, you might as well. The other obvious goal is to have the tool report average differences. (since that's going to be what most people care about). I'm happy to look at anything someone thinks is wrong. Whatever is incorrect with the formulas should at least be equal and without bias, which is good from a comparison point of view.