Yes, there is cross-tolerance between tryptamines.
In your example though, 5-MeO-DMT wouldn't affect the shroom trip very much, but if you'd instead taken shrooms instead of 5-MeO-DMT it would affect your tolerance more. You have to take into account the dose and duration of the tryptamine you take first. E.g. 5-MeO-DMT is extremely short-acting, while a tryptamine with longer duration would have your tolerance built up for a longer time.