Importance of headshell and tonearm alignment

I own a Thorens TD166MKII with an SME 309 improved arm. I haven't been able to align the arm and headshell using a protractor. The installer tried to correct the problem by cutting away the rear section of the subchassis metal base to the point of leaving the arm base supported by the two front screws. This cutting allowed the arm assembly to slide further and slightly improved the alignment but it is still off. I can get true alignment on the cartridge if I use aftermarket headshells with slots which allow the cartridge to slide at an angle within the headshell. Does anyone have experience with this type of installation and can offer a solution? Should I be concerned with the alignment of the headshell and arm or just be content with getting the cartridge aligned?