I'd recommend not installing the updater at all as it'll just bug users about updates they can't install themselves, unless you allow users to have admin rights.
I completely agree with you here. Another option is to use the Active Directory Administrative Template. We have one specifically for the Updater as well as the Editor and PDF-Tools: https://www.tracker-software.com/knowle ... -ADMX-file
An unfortunate side effect of using the MSI is that it will attempt to have multiple versions installed simultaneously. In order to avoid this you'll have to uninstall the software and install the newer version.
This should not be the case, it depends on the versions installed. The current MSI installers are designed to be able to update installations directly over an existing one, with the following caveat; it must have originally been installed via an MSI, and some older versions are incompatible with the new versions and will need to be uninstalled first. You should be able to handle this using WMI: https://www.tracker-software.com/knowle ... ic-version
the EXE allows you to update the current install without having to uninstall the older version, however it doesn't have a way to prevent the pdf printer from being the default printer, or at least the documentation doesn't provide that.
This is because the "exe" installers are really the msi installers in an "exe" wrapper that allows for auto-detection of the target system architecture. It is intended for users for whom choosing the right installer for their architecture might be a challenge. The downside of this is that this wrapper cannot pass all the parameters the MSI is capable of taking, thus:
it doesn't have a way to prevent the pdf printer from being the default printer,
If you have a mix of x86 and x64 targets I suggest managing that with Active Directory OUs or some other logical grouping. You could script a system architecture check and call your installer commands accordingly.
Moving forward, you should have few or no issues updating your MSI installed instances of the product, assuming you are consistent with the products. We have made a concerted effort to make this happen and correct the historical issues mentioned above. The Pro bundle for example installs programs from 3 products, PDF-XChange Standard (the PDF printer), PDF-Tools and the PDF-XChange Editor. If you install Pro then the Editor independently for example, you may end up with both listed in Programs and Features even though there will be only one instance of the Editor actually installed.
The solution is to be consistent with the packages you install and maintain.
I hope that helps.