Plugins of map mods often make changes to the worldspace records. Make sure to finalize the load order and make sure that the last plugin to overwrite the worldspace records (with maps) to contain all desired changes before generating LOD. DynDOLOD uses the records from the winning plugins when creating the DynDOLOD and Occlusion plugins. Do not disable any plugins, simply follow the Generation Instructions.
Terrain LOD meshes filenames are of the form ..Data\Meshes\Terrain\[Worldspace name]\[Worldspace name].[LOD Level].[X].[Y].BTR. For example..Data\Meshes\Terrain\Tamriel\Tamriel.32.0.0.BTR. In this case make sure the meshes of the map mod overwrite any other terrain LOD meshes, including the ones generated by xLODGen. Since DynDOLOD does not generate terrain LOD meshes or textures, there is no conflict with TexGen output or DynDOLOD output.
Object LOD meshes filenames are of the form ..Data\Meshes\Terrain\[Worldspace name]\Objects\[Worldspace name].[LOD Level].[X].[Y].BTO. For example ..Data\Meshes\Terrain\Tamriel\Objects\Tamriel.32.0.0.BTO.
LOD Level 32 object LOD meshes typically do not exist in a vanilla game, so by default DynDOLOD generates object LOD meshes for LOD level 4, 8 and 16. Which means, if a map mod contains LOD level 32 object LOD meshes, there is no conflict with TexGen output or DynDOLOD output.
In case a map mod contains LOD level 16 object LOD files and it is really desired to use them, then the meshes of the map mod need to overwrite the DynDOLOD output.
For quicker testing, consider generating object LOD and nothing else for Tamriel only. Once everything works and look OK, generate the LOD patch for the load order and all worldspaces with the desired options.