Depends on what type of fillets are needed . Fillets in Rhino are generally exactly circular in cross-section which may be correct depending on manufactuing system used. G1 continuity is inherent between a circular surface and an arbitrary surface. (Degree 2 is used because circular arcs can be represented exactly by a degree 2 rational NURBS).
FilletSrf in WIP/V7 now has the option of G2 blends in place of a circular fillets. https://docs.mcneel.com/rhino/7/help/en-us/index.htm#commands/filletsrf.htm?
Updated: BlendEdge is the G2 blend equivalent of FilletEge and VariableBlendSrf is the G2 blend equivalent of VariableFilletSrf
What is acceptable or unacceptable depends on the application and preferences of the user. Unequal spacing of control point is not always inherently bad. For many engineering applications changes to the shape of a surface are very undesirable/unacceptable. For aesthetic design the changes may be fine.
Trimmed surfaces can be Rebuilt in Rhino. Rebuild works on trimmed surface, and if the Retrim option is selected then the rebuilt surface will be trimmed. RebuildUV works on trimmed surfaces but does not currently have a Retrim option, which could be added. InsertKnot and RemoveKnot can also be used on trimmed surfaces, which remain trimmed surfaces.