Yes.....
If the direct charging wire broke, all of the power to run the engine would continue to flow through the bulkhead to the main junction, and from there to the igntition etc.
The only difference would be the addition of the power to recharge the battery. On a non-modified car, that's not an issue. It would be the same as stock except instead of some sort of bulkhead connection, there would be a splice. A well done splice will have less resistance than the stock terminal connections used on most years and models.
.. and no
we still need it to go through the firewall to the main junction. The goal is to do that with minimal resistance for the expected current.
In both diagrams above, the intention was to show the wires are going directly through the firewall, say by drilling a hole through the original bulkhead connector or using a grommet.
The battery only supplies power while starting and when the alternator can't supply enough.
Fusible links are there to protect against battery discharge to ground while allowing temporary high but expect current loads.
The disadvantage of a fuse on the charging wire is that it can be blown by a spike in current. Recharging a really drained battery can pull 20 plus amps for a short period of time. Yes you can use a fuse with a heavier wire, say 8 gage. That's probably OK, but we really don't want a 40 or 50 amp fuse on a 12 gage wire.
As mentioned above, unless the system is being entirely redesigned, there's no way around sending power through the firewall to the main junction. However a good way to reduce the amount of power flowing in through the bulkhead and all of the connections afterwards is relays. Heavy loads can be powered direct from the alternator tri using fused circuits and relays triggered by the original switches.
In my experience the headlight circuit is the most lightly wired on A-bodies and putting the lamps onto relays does the most good. (The factory wires to the lamps are just 18 gage, at least for most years.)
