This has been asked on the mailinglists, but no answer has come up intil today. I've build the latest xindice head (1.1beta5-dev) and installed xindice clean under tomcat and all collection tbl files are 6152KB which seems to me like a waste of space. I can also tell you that this started happening after we switched from 1.1beta3 to 1.1beta4, so I guess something changed between the two versions that messed something up.
Actually files were supposed to be created 4Mb in size, not 6Mb. File size depends on the page size and page count, which currently default to 4096 bytes and 1024 pages, giving 4Mb initial size. While page size currently is configurable via config, page count isn't.
Made page count configurable.