Another reason for different forms of advice that seem to be conflicting could be that the details of the solution often depend on the details of the application goals and requirements (and sometimes in subtle ways). For example: When someone (only) says “I’d like to render 5000 models”, then the advice would be vastly different from the advice for the case that someone says “I have 50 models, and want to render 1000 instances of each of them”.
You already gave more specific information, and mentioned that some of the models in your case are supposed to be instances (of trees). And for this, using real instancing is usually by far the most efficient solution, both in terms of memory requirements and load times, as well as rendering performance. You can look at some of the samples at GitHub - bertt/cesium_3dtiles_samples (and maybe related threads like From I3dm to EXT_mesh_gpu_instancing? ) to get an idea of how this could be accomplished.
(You also mentioned that you have the lat/lon information of models in a database, and this sounds like it could be related to Consider convenience functions to create instanced models · Issue #84 · CesiumGS/3d-tiles-tools · GitHub . There is currently no specific timeline for addressing this issue, but some of the necessary building blocks are already there…)
Options 2 and 3 sound like they could lose a lot of information that you have because of your knowledge of the structure of the scene. For example: It could be difficult to perform these processes in a way that preserves the instancing information (in the worst case, you might end up with different GLB files that contain “the same” geometry data, but that is something that will have to be investigated)
You also said that you have other (non-instanced?) models, geometry objects, and time-dependent data. It’s not clear what exactly this is. Related questions could be: Are these models “large”, so that they could benefit from a conversion into 3D Tiles and Level Of Detail? Are the time-dependent models just animated glTF files, or is the time-dependency supposed to be controlled in a fine-grained manner by the application?