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Use of boot pins after boot process is complete

The boot 0-3 pins on the F28M35x processor need to be pulled up to Boot to Flash.  Can I use these pins for alternate functions after the boot process completes?  I notice on the Concerto controlCARD the pins are pulled up with 57.6K resistors and pulled down through a DIP switch with 2.21K resistors.  Mostly what stands out is the pins are not used for anything else. 

Specificially, I want to use PF2_GPIO35 as U0TX (Alternate Mode 13), and PG7_GPIO47 as MII_CRS (Alternate Mode 15).

Any insight here would be greatly appreciated!

Paul