Does EPCS16 can configure EP3C80?

In most cases, it can. EP3C80 configuration bitstream size is 20 MBit while EPCS16 can hold only 16 MBit. This means, that the configuration isn't guaranteed to fit the device and that bitstream compression must be used. But even a highly populated design allows some compression. You should check the compression factor achievable with your usual designs to get an understanding.

Bitstream compression can be selected in the device configuration options. However, if you intend indirect JTAG programming of the EPCS device, compression must be enabled in the file conversion setup, too.