So is it possible to load bitstream in parts, enough for basic PCIe endpoint within 100 ms to conform to PCIe spec and then load a bigger design afterwards?
I once had to work with a hardware team to debug a "boot issue" where we were right on the margin due to a two-phase boot process (boot initial bitstream, check journal in flash, load active bitstream) and didn't even realize going into the debugging that we were close to the margin.
It's nice to be doing plain-old software again...
The easier thing to do would be to delay enumeration.
When I looked at the encryption format for the virtex 5 series it was quicker to reverse engineer it than it was to find someone within Xilinx that could explain it (just basic bit/byte order, what's covered by encryption, etc).
At the end of the day, FPGA configuration logic is just another state machine ;)