I will try changing SPI cable with LAN cable. Which might work better in shielding external interference.
I have already tried STM32F4xx-PIO and STM32H7xx-PIO branches. H7xx works ok on SKR3 board.
But F4xx branch is not working with tmc5160 but working in step/dir mode. I have tested ben-jacobson branch
github.com/ben-jacobson/Remora-STM32F4xx-PIO.git
who is orginal developer of F4xx branch. I have posted issue on GIT about this but didnt got reply. Didnt tested remora-cnc branch which 28 commits less than ben's branch. and since it was forked out of ben's branch so didnt thought that it will work on remora-cnc branch.
for configuring tmc5160 via spi I have to change jumpers on board for SPI. Other option is, I should remain board jumpers in step/dir mode and run external spi wires connected to stepsticks (daisy chain) to RPI, which will make really mess.