Welcome to the forum, Pavelek
I'm also considering using OTG feature of MCF51JM or maybe MCF5225x. I'm also going to use standard size B connector for PC connection and standard A connector to connect flash drive. I'm not very familiar with USB, because I have used only FTDI chips.
Yes, PC and flash drive shouldn't be inserted simultaneously. My board won't be powered from USB. I'm going to detect if 5V power from PC is present, and if present, then power from type A socket (flash drive) will be immediately removed. I don't expect very much that unpowered flash drive won't disturb PC connection, but at least nothing will smoke.
ADM869L is high side switch, which switches power to flash drive. You can use any other chip for this, or maybe even simple FET solution. MAX3353 is more useful for 3V powered designs. Flash drive should be powered from 5V and MAX3353 allows to step up voltage to 5V. Second function of MAX3353 is on/off control of device mode pull-up resistor and on/off control of host mode pull-down resistors. Host mode pull-down 15kOhm resistos can be controlled directly from JM I/O pins. You need to wire one 15K end to USBD? pin, another end to JM I/O pin. To disable 15kOhm pull-down set up I/O pin direction to input. To enable 15k pull-down set direction to output and set output pin low. Device mode pull up resistor can be controlled in the similar way if JM is powered from 5V. Or, I think it can be controlled automatically from 5V power from B connector. PC not connected - USB pin not pulled up.