First post on top makes sense, in a totally backwards kind of way.
FPOT only seems right because that is the way it has been done for years.
Probably easier to code an "append", rather than flipping and shifting & renumbering pages.
However, the traditional way is not always the best way.
Just look at the YOGB&G&PHC thread, or the B5 Mod thread, or even the P&N thread, back when it was popular.
To a lesser extent, the other 100-post threads have the same problem.
With the LPOT system, you get the recent news with no hassle. For occasional visitors, the first page is good, and for the regulars, the first post or two are the only ones they haven't read.
If you want to go diving into the history of a thread, you'd be clicking a lot, but that kind of activity is pretty rare. (Who is going to read all 39 pages to get the details of how Pirates & Nomads came about?)