There is no way to round prize amounts and have them add up properly to the prize pool for every prize pool and every prize configuration. It's just math, and it doesn't work that way for every possible scenario. Some prize pools and prize configurations will allow the rounding you choose to work perfectly. Other configurations won't work. To get those to work, you must either NOT round the amounts, or round some amounts up and some down (which still won't always work), or round them down and distribute the remainder.
The TD allows you to choose how you want to round prizes (up, down, nearest) and what to do with whatever remains. I suspect Poker Timer simply removes this choice. Which, by the way, may be considered better design for many, as too many options can be off-putting to some. But others like the ability to specify things exactly the way they want, and that's who the TD has historically catered more towards.
Another option the TD could consider would be to allow the TD to decide how to distribute the leftover amount. Might be a way to be a little smarter about it, distributing the leftover intelligently, like starting with 1st place but keeping the prize amount rounded after adding [however much] leftover to it, then adding what's left of that to 2nd place while keeping the prize amount rounded, etc, until it is all distributed.
Personally, I like rounding down and just adding any leftover to 1st place.