The big problem with using compact flash in windows/linux is the swap file useage soon write the max number of writes, with morphos and SFS filesystem the number of writes done by the os ahould only be when files physically change ie install os, applications or write a data file. I've used a CF in my efika with no noticable problems and was considering using one as the OS drive in my Peg 2.
Of coarse if you use the system a lot then eventually you will hit the max number of writes and your CF will degrade but that point will happen a lot later on an amiga or amiga like system (not counting OS4 with swap turned on) then it will with a Windows or Linux box.