Hi
On the kits that I have the PHY reset input is connected to RESET_B (the main processor reset). It may be that this has been changed on newer boards (TWRSER2) but I couldn't find a circuit diagram of it to verify. In any case, it is often useful to be able to control the RESET of the PHY in order to be able to ensure that any power-up delays are respected (depends on PHY type) and that the strap input (shared with other signals) can be forced into the correct state by processor GPIO when the PHY leaves reset.
This is not required on the TWRSER (original version) with Micrel PHY, where the RESTE_B is adequate.
If there is a conflict with the SD card WP input it may be a minor design error on the evaluation board and one would have to avoid inserting a write protected card when working with Ethernet. The boards are meant to allow first simple tests and should not always be seen as a perfect reference. It may also be that the reference SW doesn't include (full) support for the new serial board and so doesn't control the line, which would of course need to be programmed as output and driven high after reset.
In the case of the RTS line, the UART4's RTS signal can be set to either PTE27 or PTC12, so RTS doesn't need to be lost.
The Tower kit only attaches UART3 to the serial output, although there are 6 possible UARTs multiplexed to various port possibilities. Basically the tower kit shows only one or two of a large number of possible configurations and so is not necessarily suitable for basing a new design on, which will be much more flexible.
Regards
Mark