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If we follow the guide in the jupyter notebook (slcan_demo.ipynb) as indicated the build will fail.
I have compiled the modules with the folowing steps:

Start from:

sudo -i

Starting with PYNQ v2.4 the kernel source is shipped as tar.
So from the top directory extract the tar and cd into the directory:

cd /
tar xzf kernel.tgz
cd /usr/src/kernel

Then invoke the config commands:

make xilinx_zynq_defconfig
make menuconfig

The ARCH=arm is not needed since we are compiling on the arm platform.
In menuconfig select the modules as described. BUT: make sure to select them as modules (with M, not Y). This makes sure the modules are compiled as loadable modules and not kernel built-in modules (a built-in module needs to be compiled with the kernel and we don't want to build the whole kernel).

Save and exit. You can check the build flag for the modules in the config:

cat .config | grep SLCAN

This should output:

CONFIG_CAN_SLCAN=m

This should read "m" not "y" so that it is built as loadable module.

Now, in order to prepare the headers and configuration files as well as build scripts to build the modules run:

make modules_prepare

Then build the modules with:

make SUBDIRS=drivers/net/can modules

And copy the build modules to the module directory:

cp drivers/net/can/*.ko /lib/modules/4.14.0-xilinx-v2018.3/kernel/net/can/

The rebuild the module dependency list:

depmod -ae

And load the module:

modprobe slcan