What are you changing? If you're changing something in an m4 file then you will see a lot of diffs. If you're adding a new file there will be some diffs but they're not bad. If you're not doing either one of those things there should be no diffs.
I changed nothing at all, but there are 20000 lines changed when I run ./bootstrap, presumably because my autotools are newer than yours.
It doesn't affect me much: I usually only make compatibility updates to the PETSc interface and I know how to use legacy autotools if need be, but this expectation of homogeneity does somewhat increase the effort required to contribute.