Adding custom overlays to Yocto image

Hello,
after vacation was over, I continued on this issue of customizing torizoncore image.
After flashing Verdin SoM with built Yocto image (i decided to build torizon-upstream-rt docker image) and connecting it to custom board no additional CAN interface (defined in my overlay) was visible in Linux. Same overlay .dtbo works fine when running on Torizoncore images pulled from Toradex artifactory built with torizoncore builder.
Serial console outputs:

mcp251xfd spi0.0 (unnamed net_device) (uninitialized): Failed to read Oscillator Configuration Register (osc=0xffffffff).

I decided to list files in /proc/device-tree/soc@0/bus@30800000/, this are the files listed on image built using torizoncore builder:

#address-cells   dma-controller@30bd0000  i2c@30a40000  mmc@30b60000  ranges           serial@30a60000  spi@30bb0000
#size-cells      ethernet@30be0000        i2c@30a50000  mu@30aa0000   serial@30860000  spi@30820000
compatible       i2c@30a20000             mmc@30b40000  name          serial@30880000  spi@30830000
crypto@30900000  i2c@30a30000             mmc@30b50000  phandle       serial@30890000  spi@30840000

And this are files listed on my Yocto built image:

'#address-cells'   dma-controller@30bd0000   i2c@30a40000       mmc@30b50000   ranges              spi@30bb0000
'#size-cells'      ethernet@30be0000         i2c@30a50000       mmc@30b60000   reg
 compatible        i2c@30a20000              mailbox@30aa0000   name           serial@30a60000
 crypto@30900000   i2c@30a30000              mmc@30b40000       phandle        spba-bus@30800000

Lots of node that are defined in .dts are missing in Yocto build among which is also spi@30820000 node used in additional CAN. What am I missing ?