If you incorporated a reference annotation, but some transcripts/genes are still assigned to the default annotation applied by these tools, then those represent features not represented in the reference annotation. That could be because they are truly novel based on how well that genome is currently annotated.
There is a lot of QA around these tools, and the GTN has example tutorials. In the tutorials, those involve model mammal organisms with good annotation coverage, and only the known genes/transcripts were considered. This results in outputs are all fully annotated. In real life analysis, that will not always be true (good annotation coverage) plus novel data might be of interest.
I’m not sure I understand what this means. Do you mean that some transcript/genes have annotation and some don’t? If so – that would be due to novels in your data. If there is no known annotation for certain features, those won’t have a known attribute like gene or transcript name.