Programming time isn't exactly instantaneous or fast on these; SRAM cells need to all be programmed to the proper value for every LUT (2^k SRAM cells needed for a single k-LUT; k = 6 in this case), and that typically is either done online (JTAG) or through attached flash which is read on startup and/or specific commands.

If you want to upload a small bugfix without it taking 10+ hours, you need to floorplan your design and use "partial reconfiguration" techniques in order to change only part of the bitstream at a time. This requires a more advanced design flow and a bit more work, but is necessary for things like multi-tenancy or lowering turnaround times.