Some amount of customization is unavoidable. If it's restricted to making very basic changes in /etc, I don't feel too bad about it. That can be documented, backed up, and automated. It's also reasonably easy to reverse-engineer, if you ever had to do so because you lost your notes. Where things start breaking down is, if you install a bunch of complex additional software, make heavy configuration changes, introduce a lot of inter-dependencies, and have customizations that are poorly documented or backed up.
In general, you'll never be able to get these changes down to absolutely zero. Configuring SSH to follow your local conventions and preferences is a good example. And so is making adjustments that are hardware-specific. On one of my servers, I need to change PCIe timing and disable some network offloading in order for things to work reliably. That's obviously not something that Proxmox knows how to do out of the box. There is no way around making these local changes and then documenting what I did.
On another node, I want to pass through a GPU to one of the VMs. Proxmox in principle has all the required tools to do so, but you need to make some modifications to the host system to prevent it from claiming this hardware for itself. That's not something that Proxmox directly exposes and you have to make local modifications. This is obviously fragile, but it is also very powerful. Just make sure to document what you did.
