Non familiar with the field, but i think boundary layer is concerned with the fluid behaviour near boundary edge (solid boundary) as a thin film appearing with tubulence. Mixing layer is linked to the zone where there mixing of two fluid flowing or same fluid with two conditions, like:
Yes, is true. Boundary layer appears when the flow is near of solid or permeable boundary and the thickness is when the mean velocity is 0,99 Ue (exterior velocity). the mixing layer is a zone of the flow where exist mixing of fluid by turbulence and strong inflection of mean velocity profile when two or many flows are different velocity (p.e over the canopy of vegetation)
This question is described in paper of Finnigan J (2000) DOI: 10.1146/annurev.fluid.32.1.519 . Conventional similarity theory of boundary layer above rough sourface is valid well above average height of roughness elements. The turbulence structure inside canopy layer and just above turbulence elements is better accounted for by the 'mixing layer' analogy. Mixing layer develops when two interacting fluids initially have different velocities. The basis for this analogy is that there is very rapid change in wind speed between air inside and above canopy. Therefore the velocity profile is characterized by inflection point which is typical for conventional mixing layer.
Wht matters in this kind of situation ids the ratio of the channel whidth to the radius of the pipe. This ratio enters into the friction coefficient (pressure gradient divided by rho u^2, u average velocity in the pipe and rho mass density of the fluid . THis ratio is plotted as a function of the roughness in the book of Schlichting for instance. It was found by Chézy in the mid eighteenth century that the friction coefficient (or Chézy coefficient) depends on the vegetation on the river bottom. You can also find information on this topic in the textbook by Pope on turbulence.