Your assumption the IPv4 is always encapsulated by ethernet is flawed. Don't confuse the network layers. Ethernet, a layer-2 protocol, can carry any numbers of layer-3 protocols, not only IPv4. On the other hand, IPv4, a layer-3 protocol, can be carried by any number of layer-2 protocols, and it doesn't care which. Some layer-2 protocols on which IPv4 is carried have larger maximum MTU sizes than does ethernet.
Ethernet and IPv4 were developed and released at about the same time, but by very different groups. It was not obvious at the time that either would end up being the dominant protocol for its network layer. Ethernet is a LAN protocol which was mostly used for IPX, and IPv4 was usually used on WANs to connect large university computers.
IPv4 can be fragmented by routers in the path, IPv6 cannot, but it specifies a minimum MTU of 1280. Lately, there is PMTUD which discovers the minimum MTU in a path before sending packets out along the path, so that packet sizes can be adjusted to fit the minimum MTU of the path before being sent.