I've been doing digital design for Xilinx FPGAs, as well as IC design, for a few years now and never had any trouble with the Linux toolchain. I can't even imagine switching to Windows and trying to automate the build (not saying it's not possible, it just seems a lot more convoluted).

It's true that smaller vendors like Lattice seldom provide Linux software, but it's also rare to find bigger shops (as opposed to hobbyists) who don't use Xilinx or Altera exclusively, and Linux at that.