Not charging after MSD 6AL installation.

The reason I get same voltage reading on alt and battery is the Ammeter bypass I did.
No.
The reason they should always be at the same voltage reading is because they are connected at all times.
Everything in the main circuit should be at system voltage and there is no off switch. Accidently touch anything in that circuit to ground and sparks will fly.
The only time voltage drops is when current is flowing through resistance. Resistance can be purposeful like the ballast, a light bulb or an electric motor, or it can be due to poor connections or degraded wires.

I don't care how it is wired. The connections and wires of the main circuit need to be large enough and good enough so there is little resistance even when lots of current is flowing. Lots of current for a '69 would brake lights on, headlights on, wipers and heater blower running.
I think some confusion comes from the fact there are two power feeds. One from the battery, the other from the alternator. They are always tied together in some manner.
When the battery needs charging, the alternator feed supplies the battery with power. Then the battery feed becomes the charging wire and current flows into the battery.

Regardless, if the alternator Batt stud and battery post are at noticibly different voltages, there's resistance in the flow path. Then you have to figure out what the path is, and then find the resistance.