Very good point on the need of objects with relationships, instead of rigid workflows!

On your challenges with precise protein concentration measurement, you might think of additionally evaluating those by NMR. It has limitations of its own and is more laborious than UV, but gives very precise results. And due to intrinsic properties of the method contribution of aggregates is naturally excluded from obtained values. (however the same property creates an upper limit for the size of the measurable particles).
Here approximate procedure is illustrated for nucleic acids, but the same applies to other biomolecules as well: