--- EDITED on Apr 29, 2015 ---
Q. My first question is, does USB HS module use ULPI_CLK input in any way? Or, in other words, does ULPICLKOBE determine not only whether the internal clock will be output but also whether external clock will be used or internal one.
- Since ULPICLKOBE has been changed to reserved, that means internal clock is NOT suggested to be used for USB HS module (default value of ULPICLKIBE=0, the clock buffer is disable). By looking at Fig.5-9, you can see how the ULPI CLK works.

Q. Can I use a different transceiver that uses ULPI_CLK as input and generate the clock in the MCU and provide it to the transceiver using ULPICLKOBE? (or was it removed from the reference manual because it shouldn't be used?)
- I think it should not be used as you said it was removed from the RM.
Q. And the last question, if USB HS module does not use ULPI_CLK input at all then could there be problems caused by phase mismatch between transceiver and the module?
- no idea