Amino acids are the building blocks of protein and they are teeny tiny and don't have the same properties, equating them is like saying a pile of old bricks is the same as a house. Ditto whole proteins (large, cannot penetrate) behave differently to hydrolysed protein (small, can penetrate or stick to the surface).
If I have found the right list the TJ conditioner doesn't look to be ideal for co-washing, not rich in cleansing emollients/ emulsifiers (fatty alcohols nor cationic surfactants) so it's possible you were simply experiencing product build up. Also washing with protein can be different to conditioning or treating with protein - washing you focus on the roots which likely don't need protein, conditioning/ treating you focus on the lengths or ends which are more damaged.
Parting with fingers is similar to parting with a comb, don't part but let your hair fall naturally. I like mine best when it falls into almost a zig zag or diagonal. As you say scrunch, diffuse upside down to part dry then pin or clip off your face or slightly to one side for the best curl and root boost. AFAIK
curly hair salons don't part the hair.