It seems to me that the reason for dpkg-source applying patches slower than plain "quilt push -a" is that it invokes quilt once for each patch. Perhaps quilt does some preparation on each invocation and when called multiple times that accumulates.
(mkdir glibc-2.9/debian/source; \
echo "3.0 (quilt)" > glibc-2.9/debian/source/format)
$ time dpkg-source --without-quilt -b glibc-2.9
...
real 1m6.618s
user 0m24.906s
sys 0m45.139s
$ time dpkg-source -b glibc-2.9
...
real 1m45.576s
user 0m40.831s
sys 1m3.688s
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