microcontroller vs parallel port

I don’t think bit banging SPI over the Parallel Port is going to have the required speed.

If you want to use the Parallel Port to talk to a motion controller board EPP is the way to do it.

This has a couple of options.
Easiest is to grab a Mesa 7i90 72 io pins and 3.3v to 5v logic translation is built in.

Next easiest, grab a Spartan 6 dev board and modify the 7i90 firmware, this the way I’ve gone, in actual fact not a lot needs to be done. I also designed and built some boards to do the 3.3 to 5v translation. One of the Popular colorlight boards, RV901T, can also be used, but this requires replacing some SMD chips and running the board from 4.2v. Experimented this with SPI, EPP would be doable but with reduced io. I’ve used this board as a Smart Serial board.
Third option would be EPP to micro controller, this would be the most different as the driver on the linuxcnc side would have to written from scratch and the firmware from the micro controller would have to be written from scratch as well.
SPI is best suited to the RPi 4, until something can be done with the RPI5.

Although one of the PCIe to parallel\serial port chips does have SPI capability, but as far as I am aware the only boards available are from the chip vendor. And yes this does appear to be implemented via hardware on the chip.

Now let’s talk the economic side.
Given the choice of buying a 7i90 from Mesa or rolling my own Mesa would have been the choice. The cost of developing isn’t cheap compared to buying a ready to go product. PCBs need to be designed and manufactured, parts need to be bought. Another big kick is the postage to Down Under.
If you can get onto a project that is mature, the costs can be a little less. But a lot of the time the electrical interface from 3.3 or 5v logic to 12 or 24v for inputs from and to your machine are left up to yourself.
It’s a lot more than choosing a particular board and writing software, there’s a few more hats you have to wear to get a project going. Those that do my hat is off to you.
Regarding USB, user wez is working on this and does seem to be having success.

One thing I have been grateful for is the help Pete from Mesa has given to get the Mesa firmware running on non Mesa hardware. He’s really a generous bloke.

Will "AVR over SPI" remove paraport limitations e.g. speed (encoders sampling etc.)? Or paraport itself is the bottleneck no matter how fast sampling device attached to it?

If you do want to try bit banging SPI
www.n5dux.com/ham/files/pdf/SPI%20And%20...20Printer%20Port.pdf

www.wallacecompany.com/machine_shop/EMC2/serial_adc/
www.wallacecompany.com/machine_shop/EMC2/serial_dac/

Aforementioned PCIe card
www.asix.com.tw/en/product/Interface/PCIe_Bridge/AX99100