If aspartic acid residues are densely packed and the distance between their side chain functional groups is close, I believe that the pKa might upshift to reduce charge repulsion. Is my understanding correct? Additionally, are there any papers that address pKa shifts in amino acids within proteins based on their surrounding environment?
The pKa is defined with respect to the solvent in which the acid is active, i.e. the pKa in water is different from the pKa in ethanol. Among the approximations behind all equations is the one that the change in the concentration of the solvent does not change considerably, e.g. that the concentration of water is always 55 mol/l. If you leave the range of this (and your scenario sounds like this), you need to work with a "regular" thermochemical equilibrium constant K=[A-][H3O+]/([HA][H2O]) instead of KA=[A-][H3O+]/[HA]