I would assume Proj4 does a no-op if the source and destination SRSs were the same, but maybe it doesn't. If it's reprojecting, it does some reasonably complex calcuations on every vertex of every geometry, which would explain the added time.
In https://trac.mapnik.org/ticket/138 I added a no-op around not calculating extents for same-SRS map/layers, but maybe proj_transform should do a similar no-op rather than pass it through to Proj4? Rob :)
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