Why no "omnibus" versions if they comprise a single, complete story?
I have seen more and more indie books being released as serials and then an omnibus will be released once complete.
As for a direct answer, I looked through my TBR list and the list of books I got for free; out of the indies, the longest appears to be
Anu-Bis by T. O Bolseen at 824 pages long. There are a couple longer ones but they don't appear to meet your criteria for no-omnibuses. There might be longer ones in there too, but I only started marking things as indie or not a few months ago.