Electronic – Can the microcontroller program flash memory be used for storing user configuration

There are PIC24 & dsPIC33 models with 512KB flash.

PIC18F8622 & 8722, and some other PIC18F's (87J50, 97J60, for example) have external bus interface, you can put a parallel flash (29xx-type) there, and the external bus can address up to 2MB.

From the datasheet, we can see that this can be used to store program code:

The External Memory Bus (EMB) allows the device to access external memory devices (such as Flash, EPROM, SRAM, etc.) as program or data memory.

Using other types of interface to connect to an external flash might be problematic as you would not be able to run the code from the flash directly, instead, you'd have to copy the code into RAM before running it - but since these microcontrollers have extremely limited RAM resources, this would severely limit the usefulness of such a solution (you'd have to implement some kind of paging/overlay technique).

Here's Microchip's product selection tool, allowing you to search for models with certain features: http://www.microchip.com/maps/microcontroller.aspx

If you are using the FPGA with an industry standard type of SPI Flash chip then it is possible to use the SPI Flash chip in the way that you describe. The way to do this with the most user control is to put a small MUX Chip between the FPGA and the SPI Flash chip in the path of the SPI Flash control signals. The other side of the MUX is then connected to alternate user activated pins to support an alternate SPI interface to the SPI Flash chip. You would then program your own interface into the SPI device to access as desired.

On the other hand Xilinx has a detailed App Note that shows how this can be done in a more generic way without the added MUX. See http://www.xilinx.com/support/documentation/application_notes/xapp694.pdf.

A more directed document for the Spartan 6 FPGA family is here: https://www.xilinx.com/support/documentation/user_guides/ug380.pdf