Ganapatya school is very ancient. That Mahabharata says something does not make them heterodox (or heretic as you seem to be hinting at?). Heterodox with regard to what?
In Atharva Samhita, for example, Ganapati is tied to balagrahas along with Skanda, and these Samhitas are older than Bharata. The most celebrated philosopher, Shankaracharya, dismisses Vinayaka in his commentary of Gita as ‘bhuta’ - भूतानि विनायकमातृगणचतुर्भगिन्यादीनि यान्ति भूतेज्या भूतानां पूजकाः. Several hundred years later, all major monasteries established by Shankaracharya invoke Ganesha regularly, ignoring his statement in Gita Bhashya.
The understanding of these deities changes, based on the capacity of the observer, as also the social and cultural contexts at that time. In the Vedic age, Indra was the prototype of perfection while Mahabharata reduces him to an inferior demi-god. Those not eligible for Tantra, dwell on stories and myths (which are certainly of value too) - but Tantra is not about them - it is about archetypes, using practical methods to realize the deity, and become the deity. Acharyas of Ganaptya sects such as Herambasuta and Girijasuta reached heights of Siddhi that most people lecturing on Mahabharata and morality will probably can never ever even imagine.
The point is - there is no mainline Hindu tradition really. Whatever gets perceived as mainline does not date back to anytime earlier than say the sixteenth century. Manu Smriti prescribes whipping women who leave the home without husband’s permission, or boycotting a Brahmana who works for non-Brahmanas and so on. Now, is that “mainline” Hindu tradition?
The beauty of Hindu tradition is that there is no one tradition - one book that dictates A to be true and B to be false. So, your line of thought separating orthodoxy vs heterodoxy w.r.t Hindu tradition seems inaccurate.