They're usually at around the same level but the newer WCs have their overflow as part of the siphon valve so will be lower. As long as the WC flushes and the water stops before the overflow level and uses 6 litres then there's no real issue.
To comply with the water regs, overflows must be below the outlet of the fill valve so that water cannot accidentally be drawn into the supply. Same goes for cisterns in the loft. This is a very old rule dating back to the water byelaws of the 1880s