Did you check if the program actually saved the changes in the file, or maybe created a new file at a different location, so the original file still loads last? It's been a while since I used the Model Tweaker, but it might be better to save the file with a new filename, put it into a dedicated folder, and then create a new SC4Desc file with the Plugin Manager or PIM-X, which should reflect the resized model dimensions as well. Finally, make a new lot, the grey box in the Lot Editor should have the desired size then. If you don't see a grey box in the original lot, that usually means the building has been added as a prop, or the model size in the SC4Desc file has been set to 0 manually.