Windows only tools? You must have been using Altera options (I briefly maintained the page for Quartus compatibility at wine, circa 2004). Even them have had Linux support for a while, Xilinx has Linux support for as far as I remember, at least some ten years.

The ecosystem is terrible, I agree with you. However, the lock in is restricted for the final synthesis part. Simulation is mostly done with (very expensive) third party tools, such as Mentor Graphics Modelsim, and in professional settings the build is automated to a point that opening the vendor's GUI is frowned upon.

There are some quality open sources tools on FPGA build automation, but most places I had contact with have their own internal tools.