The CR encounter system is not an exact science
I think, overall you are worrying too much about getting the exact point values calculated here. In our group's experience, a typical party can endure much more than the XP value of a deadly encounter, and there is wide disparity about how dangerous a monster of a given CR and XP value actually is.
You can even see it from the rules themselves, which provide the same x2 XP multiplier for 3 monsters and for 6 monsters -- that is twice as many monsters, which are able to deal twice as much damage, have twice as much hp, etc., for exactly the same XP value.
That being said, there is no rounding down involved. What point 5. of the process says is:
5. Compare XP. Compare the monsters' adjusted
XP value to the party's XP thresholds. The threshold
that equals the adjusted XP value determines the encounter's
difficulty. If there's no match, use the closest
threshold that is lower than the adjusted XP value.
For example, an encounter with one bugbear and
three hobgoblins has an adjusted XP value of 1,000,
making it a hard encounter for a party of three 3rd-level
characters and one 2nd-level character (which has
a hard encounter threshold of 825 XP and a deadly
encounter threshold of 1,400 XP).
That pretty much explains it. For example, you have three 3rd level characters that have a value of 225 XP for hard, 400 XP for deadly, and one 2nd level who has 150 for hard, 200 for deadly. Summing them all up you get 3x225+1x150= 825 for hard, and 3x400+1x200=1,400 for deadly.
The monster has an XP value of 1,000, which is above the threshold for hard for this party, and below the threshold for deadly. In that case, the encounter is considered to be hard. You need to clear the threshold for the category to have it counted as an encounter of that category. That means there is a range of XP values for this party that all count as hard, from 825 XP to 1399 XP.
This is unavoidable and intended -- there need to be ranges for each category, because there are many different XP values for encounters, and if you just have four categories, you need to group those XP values into ranges for them. You do not need to remove any enemies to get close to the lower end of the XP range.