Certainly Modern Bon is very similar to some forms of Buddhism today but that still doesn't make its refuge worthy. As you know at every age of the turning of Dharma the Dharma of the previous age becomes extinct and is renewed again by the Tathagata in this case Shakyamuni Buddha so for one to suggest that there is a ancient Buddha who's Dharma has been preserved in the form of the Bon religion is nonsense. Buddhist Refuge comes from Buddha you cannot call yourself a Buddhist if your refuge is also placed within Bon as well that's taking eclecticism way to far.
Of course everything samsaric has a beginning, middle, and end; and the Dharma of transmission is one of those things I guess (?)
We are told in many many places that the teachings of Shakyamuni will eventually die out.
However I'm hesitant to take the timelines we're given for this degeneration literally. For example, in one source I read (I believe) the Buddha himself said if women were allowed into the Sangha, the Dharma would only persist in this world for 500 years (as opposed to 1000?). That puts the total degeneration of the the teachings somewhere around the time of Christ. Which, I'm sure, makes sense to some people. Other sutras that comment on this clearly put the TOTAL degeneration of the Buddhas teachings long before our present era. Others don't. Most of us don't seem to care too much about it, and go about our practices anyway.
Moreover, so many things we believe (Padmasambhava living 3500 years, for example) are easily excused as "nonsense" by those who are looking for reasons to dismiss our tradition, whether within Tibetan schools or from the perspective of other Buddhist or even scientific views. I'm just arguing that we're all in this spectrum of beliefs. There is nothing that can't be seen from the perspective of ME and NOT ME and drawing lines in the spectrum of teachings related to and informed by Buddhism (there are so many!) and saying "that's us
! thats not-us
!" seems hazy most times, especially when people adhere to the core teachings and then have many other methods and traditions that inform their manifestation and practice. I.E. there is no Buddhism that exists in a vacuum: it is always placed within a particular (worldly) context of objects, language, and "degenerate" concepts.
I admit however that, without the refuge, a path can't really be called buddhism. Without Bodhicitta, it can't be called mahayana. However, if the view is correct and the ultimate refuge is...nondual, beyond words, unexcelled enlightened being, how can we fuss about that?