(1a) ChipIgnite projects like IEEE-SSCS are
not flip-chip, but are wire-bonded into QFN packages; plus you get back some bare die that you can do with as you like. There will be nothing obstructing the photodiode.
(1b) The photodiode has always been in the PDK; it's just that there is relatively little information about it other than a page of DRC rules.
(2) In magic, you can use the "fillblock" layer to avoid any fill over the device (you will need to run the command
tech unlock *
first (I should have thought to add that to the photodiode device generator).
I am very interested in seeing photodiode designs fabricated and measured so that we can get some useful information about the devices.