I've done similar on a small downstairs toilet in the past; I took up the toilet pan so that the fitter (lazy me) could lay the lino, when this was down I refitted the toilet, sealing around the base of the pan with a clear silicone sealant. This gives a clean, professional job that's easy to clean. The fitter (or you) will be glad not to have to cut the lino around a fixed WC pan. I'm doing another similar job in a larger bathroom and I plan to fit the lino myself this time, I'll use a Floorwise adhesive (specially for vinyl coverings) to stick the lino down around threshold, fittings etc.