With most distros, you have to download the kernel source code, insert the ACS patch, and compile+install the patched kernel.
Since you are running Ubuntu(or spin thereof), there are pre-compiled kernels with the acs patch available here-
https://queuecumber.gitlab.io/linux-acs-override/
Download the kernel and headers, and install them with sudo dpkg -i <file>.deb, obviously substituting the correct path for it. Put pcie_acs_override=downstream in /etc/default/grub in the line GRUB_CMDLINE_LINUX_DEFAULT=" ". Then run sudo update-gruband reboot.
Hopefully, then they will be separated.
If you want to learn to compile your own custom kernel, you can download the patch at the page above. Download the patch for the kernel version you will be compiling, the patch versions are very similar but with minor tweaks.