CONF_DONE as input?

CONF_DONE is an input when multiple FPGAs are configured sequentially; as each FPGA configures they release their CONF_DONE driver (which was driving low) and then wait for the CONF_DONE signal to go high before entering user mode. This ensures that all FPGAs enter user-mode once configuration of all devices is done.

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I'd like to be able to delay entering user mode, after configuration has finished, and I wonder if I could do that by holding CONF_DONE low

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Yes, this is ok, and used to be stated in some of the device handbooks.

Cheers,

Dave