No, there is no way to avoid the application of the small time steps to all components of the trajectory using the ODE integrators of Matlab. The only exception is, that the integrations can be separated, if the different components do not interact with each other.
This is a common problem at simulation large system, e.g. the global weather, a organism with resolution of single cells, the mass distribution of the universe, or a vehicle simulation considering high frequency vibrations of small elements. If you want to simulate the whole system, the part with the highest frequency determines the step size.
It is possible to create integrators, which identify high frequency parts dynamically. Then these parts are integrated with a smaller steps until the changes reach a limit, in which the other components are affected. The implementation is hard and needs some heuristics, because the identification of the low and high frequency parts require to simulate the system at first...
Using a vector of tolerances is equivalent to scaling the components, e.g. if a certain component is measured in meter or nanometer. This influences, how the different components are used to determine the step size, but again the steps are applied to all components.