<!-- Include additional build rules for an Office application add-in. -->
<Import Project="$(VSToolsPath)\OfficeTools\Microsoft.VisualStudio.Tools.Office.targets" Condition="'$(VSToolsPath)' != ''" />
Edit a renamed copy of the referenced .targets file (in my case, the file resolved to C:\Program Files (x86)\Microsoft Visual Studio\2017\Professional\MSBuild\Microsoft\VisualStudio\v15.0\OfficeTools\Microsoft.VisualStudio.Tools.Office.targets and I made a copy Microsoft.VisualStudio.Tools.Office_FIX.targets in the same folder - didn't check if it works from a different folder).
Find the GenerateApplicationManifest element and change its attribute Dependencies="@(DependenciesForGam)" to Dependencies="".
Change the section found in 2. to reference your edited .targets file instead.
This will have to be repeated whenever the version of the .targets file shipped with VS is updated (or you won't get the updates), but I'm hoping it will be fixed soon...