Yes, that's right. I'm suggesting CONF_DONE can be treated separately.
however, there is an important consideration which is going to contradict what I've already said, something that I was reminded of after a little further reading...
When the FPGA releases CONF_DONE it enters user mode - the mode in which it starts doing what you want it to. If your design makes use of any of the pins used for AS configuration your code is going to take over the control of them. They will start doing whatever you've designed them to do.
Assume you have two devices. The first boots and enters user mode while the second FPGA continues to boot. If the first device makes use of the AS configuration pins (it may wish to access the EPCS as part of its design) and it attempts to do so then the second device is not going to boot successfully.
By ensuring CONF_DONE is common across all the FPGAs booting from a single EPCS, you are guaranteeing none of them enters user mode until the last device has successfully booted. The last device in the chain will hold all CONF_DONE pins low preventing any of the FPGAs entering user mode until it has booted.
However, there is a further complication. Once a device enters user mode the DCLK pin is under user control. If the first device in the chain is responsible for generating DCLK during configuration then, once it has entered user mode, it is going to stop generating clock cycles - preventing the other devices from booting. Is the first device in the chain responsible for clocking the EPCS? I don't believe that is explicitly clear from the documentation, but I suspect it is.
See: serial configuration (epcs) devices datasheet (
http://www.altera.com/literature/hb/cfg/cyc_c51014.pdf)
Figure 4 implies this is the case, but no description explicitly states this.
What might clinch this categorically is control of the nCS pin on the EPCS. This only comes from the 1st FPGA. Once it enters user mode is will not (necessarily) control this pin in a way that allows the other FPGAs to boot.
So, to go full circle - I recommend to do short the CONF_DONE (and nSTATUS & nCONFIG) pins across multiple devices when booting them all from a single EPCS - as per Figure 4 in the Serial Config Datasheet. If you really must have the FPGAs enter user mode independently of each other, boot each from their own EPCS...
Regards,
Alex