Sorry, but it sounds like you aren't cut out for transformer based LLM research if you can't interpret the results.
Each layer in a transformer has its own KV cache that feeds from the previous layers output. Those internal layer activations are not subject to training loss directly. The model can spit out a dot but still perform additional computations within those layers.
The dot effectively prevents information from flowing from the final layer into the output, but all the intermediate layer activations are still available for future tokens. The limitation here is that information cannot be passed from the last layer to the first layer.
If a long running calculation needs to go through all layers and then be refined further, CoT becomes mandatory because CoT tokens are the only way to pass information up to the first layer, but since they are not as information dense as the internal activations, replacing them with a dot does not degrade performance as much as one would expect.