If we have a patent which is violated if the bundled software includes a feature but isn't if the software is separately installed later, by what argument is that a rational patent? Where is the huge philosophical leap between a tool within the platform and an extension which plugs into the API?

The simple answer is, as we all know, that there isn't, and that they've wrapped some fancy language for a general purpose computer around regular expressions (which very substantially predate the patent) and managed to get the patent granted. This is ludicrous.