This is a good question, and the answer is, aerodynamic resistance is not defined inversely. It is rather, defined in a context that is often misinterpreted.
In your question, you state that aerodynamic resistance is basically how much the roughness of the surface slows air movement down. This statement is not correct, and it seems to stem from the misinterpretation of context.
A monograph by De Groot (1963) also shows that molecular transfer processes have the general form analogous to the electric circuit shown by @Deditos' answer:
$$
Flux = \dfrac{Force}{Resistance}
$$
This is also true for air-sea and other general fluid-fluid interfaces. Flux is the transfer of a quantity (say, momentum, enthalpy, mass, etc.) through the interface and the associated boundary layers (say, air, water, canopy, soil, etc.). In the electric circuit analogy, force has the character of potential gradient and resistance has that of the inverse conductivity. The important point to be made here is that resistance is not resistance of interface to the aerodynamic flow - what we would intuitively imagine as friction or stress. It is in fact, resistance of the interface to the forcing. In case of momentum, this means that given equal forcing, higher resistance yields lower flux. Thus, lower resistance translates to rougher surface. This is why forest has lower resistance values than grass or open ocean.
Example: Given equal forcing, rougher surface results in higher stress compared to smoother surface. It can be said that the rougher surface is "more permitting", or "less resistant" of momentum flux.
In the electric circuit analogy, Flux, Force and Resistance are symbolic, conceptual entities. Force is not necessarily in $\rm N$, and may be a temperature or humidity gradient like it is given on slide 16 in the presentation you linked. Resistance may thus take different formulations.
Note that nowadays, in both modeling and theory, we often use exchange coefficients to characterize momentum $(C_{D})$ and enthalpy $(C_H$, $C_E)$ fluxes through the interface, which act as conductivity and not resistance. For example, in case of momentum:
$$
\boldsymbol{\tau} = \rho C_{D}|\mathbf{U}|\mathbf{U}
$$
where $\boldsymbol{\tau}$ $(\mathrm{N/m^{2}})$ is vertical flux of horizontal momentum (wind stress), $\rho$ $(\mathrm{kg/m^{3}})$ is air density and $\mathbf{U}$ $(\mathrm{m/s})$ is wind vector at some reference height above the surface. $C_{D}$ (non-dimensional) has different values depending on the surface properties.
In that particular presentation that you linked in your question, it is not clear to me why resistance $r_a$ has units of $\mathrm{s\ m^{-1}}$. For sensible and latent heat flux $\mathrm{ (W / m^2) }$ formulations on slide 16, the units don't quite work out, but it is possible that the equations shown were more illustrative than exact. Because bulk flux formulae are most often based on theoretical, empirical and dimensional grounds, $r_{a}$ can be defined in various dimensions (units) depending on the bulk flux formulation.
Reference:
De Groot, S. R. Thermodynamics of Irreversible Processes. North Holland Publishing Co., 1963.