IME, all of those pins can be left floating on MachXO2 devices in the default configuration. JTAG is enabled by default, I don't remember how you use JTAGENB, but I sure left it NC on my boards and never had a problem. I actually left ALL of the pins you mentioned NC, and it's OK for JTAG configuration.
Not sure what the DONE pin would give you here if it's just for visual feedback. The programmer itself will give you feedback when Flash programming is done. Then, MachXO2 devices are fully configured (ready to work) in just a few ms from Flash (as opposed to some FPGAs using external Flash, which can take hundreds of ms), so the visual feedback would not serve much purpose IMO.
The above pins are probably to be considered in cases where you want to use other means of programming on top of JTAG (SPI...)
I (very briefly) re-read the MachXO2 programming guide, and it looks like the usage of the above pins is described in it. Not just in one place though (a bit spread out), so you'll need to search for the pin names in the PDF to get what purpose they serve.