Disclaimer: I'm neither a drummer, nor do I play very much metal
Don't make it a habit to always connect the same foot with the snare. Good metal drummers have a high degree of independence between hands and feet, basically they can switch the pattern of feet around at will as long as fast sequential beats alternate both pedals.
That said, the “default” pattern, like with hands (in a right-handed drummer) is to first assign the right foot to the most important/strong beats and then use the left foot to fill the gaps. This makes sense especially for beginners of double-bass, because the right foot is already well-trained, so you have a good rhythmic and dynamic foundation. That makes it pretty obvious what's wrong when the left foot is e.g. a bit too late. OTOH, if you immediately give the left foot the leading role, chances are that the whole groove is a bit off and it is much harder to figure out the real issue.
Furthermore, even for experienced drummers the right foot typically has more dynamic control and simply more power, which again means it makes sense to give it the lead role.
It just so happens that in the groove you're talking about, the right foot stubbornly falls on all the strong beats, including the ones that also have snare. But that's not because the right foot is deliberately matched with the snare, but just because it occurs naturally.
If the coincidence of snare and right-foot-bass drum throws you off, then just work on this. Also practise some beats where the snare coincides with the left foot (or simply not with the kick at all), but again: don't make “never right foot and snare together” a habit.