I think the fact that Neil is not the biological father is 70% proven. The characters emphasize several times that Tremolo does not look like his own father, the relationship between Lynette and Neil is similar to friendly, but not romantic. On the other hand, I do not know how DPC can show this without hurting the feelings of the ANTI-NTR Guard. Lynette is too young and clearly doesn't have a romantic partner. Perhaps at some point, MС leafing through the diary finds out that his mother is pregnant, although his father and Lynette have not even started dating yet. Her boyfriend was a rich jerk who immediately left her, and Neil, as a good guy, promises to raise someone else's son as his own.
It would certainly be a good drama if it turns out that Rusty and Tremolo have the same father, for example. They would become brothers not only by brotherhood, but also by blood. It would be beautiful.
Tommy is only Josie's half-brother, this is clearly done for a reason, so Tommy can also be MC's own brother.