If you have the alternator connected to the fuse box, and the battery connected to via a different route to the fuse box, and something in the fuse box becomes grounded, the current will flow from whatever source is available through the wiring to ground. Now, I'm assuming that the your alternator is connected to the fuse block through the two 2.5mm^2 wires, and the fuse block is connected to the terminal box through two 2.5mm^2 wires, and the terminal is then connected to the starter through a 6mm^2 wire to the starter, and a 25mm^2 wire to the battery. The negative post of the battery and the alternator are both ground, so they are in actuality wired in parallel to the fuse block. So no matter where the faulted ground occurs, current will flow from both the battery and the alternator to the fault.

The current carrying capacity of the two 2.5mm^2 wires together is roughly equivalent to the single 6mm^2 wire. If you are really concerned with the amount of current flowing to the fuse box from the alternator, see if you can move the wires from the alternator to the terminal block, and wire the alternator directly to the terminal block. That way you have four 2.5mm^2 wires to the fuse block. If you are really, really concerned, stick a 100/80/?? fuse in-line.

Regardless of how you wire it, if you short an unfused wire to ground, you are going to have a fire hazard whether you have a larger alternator or not. In fact, a larger wire would likely be more of a fire hazard since a smaller wire will fail sooner, and the larger wire will continue conducting and heating longer. I know you're trying to be safe, but I would humbly suggest that you are overthinking this. If this were a legitimate issue, you would be hearing about people having to replace wiring in the unfused portion of the circuit more often, and underhood car fires from insufficient wiring. My guess is that there is more of a hazard from frayed wires arcing and sparking at low currents that don't draw enough current to blow a fuse or burn out the wire than there is from the unfused power feeds. As long as the connections are secure, and the wires are strapped down to prevent chafing, and the wires are located away from strong heat sources (e.g., the header) and moving objects (pulleys and belts), then there is no reason to worry about the larger alternator. The battery has always been able to provide more current than the original alternator and the current wiring has proven sufficient.

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mjk

'84 300SD 119KMi (Liesl der Diesel)
'84 300D 326KMi when the oil left (former parts car)
'82 300SD 253KMi (new parts car)