You mean because Quicklogic uses an OTP-Solution and Xilinx devices are reprogramable?
I don't know the Quicklogic devices in detail, but I guess they are using so-called Antifuse Technology.
One reason for such solutions is speed. In an SRAM/EEPROM-based device the junctions of the interconnect are made by transfergates and/or multiplexers. This costs time. In antifuse technology, connections are created more or less statically during programming.
Another advantage of antifuse over the other technologies is that you do not need to have a memory cell that says whether some switch is "on" or "off". That is, you save chip area which makes it cheaper for production. Less power is needed as well.
The reason why logic is implemented in a different manner might be induced by the basic technology. In an SRAM-based device it is perhaps more efficient to go the LUT-way. Another interesting side-effect here is that one can use the LUTs as small RAM-blocks in his design.
While a LUT could be made well out of antifuse cells, a multiplexer structure yields perhaps to better speed characteristics. But I'm not the expert here.
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