Iâ€™m no expert but I tiled our en suite floor first and the plumber installed toilet etc on top - much easier than cutting tiles to fit around plinth and neater too.
After tile cement and grout have set hard, rest WC in place and mark tiles through fixing holes, remove WC and drill mounting holes (I find spear bit meant for drilling glass is great for use on tiles too). Then screw in place with stainless steel or brass screws being careful not to overtighten and crack WC. Finally run silicone sealant around plinth/tiles junction.
Iâ€™ve fitted cork tiles around a couple of toilets but marking and cutting an accurate profile takes time and I'd avoid doing so with ceramic tiles if possible.
I would advise you to lay the floor tiles first. It will look better and be easier tiling wise to save you shaping the tiles. Also it enables you to change the suite in the future as you wont have a gap in the tiles when you take the old suite out because most toilets and pedestals are different shapes.
Its worth noting that in the best bathrooms most tiling - floors and walls - is carried out prior to fitting sanitary ware. This not only makes tiling easier but it enables sanitary ware to be changed. Sanitaryware should also be centred symmetrically on tiles where possible and this means planning positions for appliances and the tiles together.
Putting a toilet on the tiles also puts the toilet at the correct design height which is fairly standard at 40cm.