MCU controlled power-on sequence
If you want your LDO being off during startup, you will have to ensure its EN pin is low. That's the reason this thing has one of these.
Leaving it floating is nothing I would consider for a professional device.
If you are concerned by the current draw of the 10K pulldown, consider using a bigger one. 200k or more. Should be more than enough to pull EN consistently down.
Clock output is different, I don't see a reason of pulling a clock line down. Won't start oscillating on its own.