David,
The primary objective is to eliminate (or minimize as much as possible) having wire that is unprotected from continuous excessive current in case of a short. Generally that means placing the circuit protection device (fuse or CB) as far upstream as possible, i.e. as close as possible to the power source. So in typical load circuits the answer seems obvious and intuitive, since the power source is at one end and a load is at the other end.
In case of the alternator B-lead, the answer is a little less obvious, because you have what are potentially power sources at both ends of the wire: the alternator at one end, and the battery at the other (ultimately, on the other side of the master relay). But the two are not equal. This requires a closer look. Under normal operating conditions, current flows from the alternator toward the battery. But in case of a short circuit condition, the greater concern is about current flowing from the battery, not from the alternator. Why? Several reasons, two major ones being:
1) Max short circuit current: The B-lead wire should be sized appropriately to safely handle the max current output the alternator is capable of delivering. This is a requirement even for normal operating conditions. But, conveniently, this also covers the short circuit case as far as the alternator is concerned. If a short circuit occurred and the alternator was forced to drive its max output current directly to ground via the B-lead wire, well, the B-lead wire should be able to handle it because we sized it that way. Whereas, on the other hand, no wire on the airplane is sufficiently sized to safely sustain the max short circuit current that the battery can produce, which could approach 1000 amperes. Battery short circuit current through any unprotected wire on the airplane does create a very real fire hazard.
2) In terms of electrical system architecture, the battery is the central power source and the alternator is secondary, in the sense that the electrical system can readily operate on the battery without the alternator, but not vice versa. (And another way to think of it is that the alternator circuit is just another "load" circuit, which happens to have the unique ability to also source current rather than just sink it.) Therefore, thinking of the fuse in question, it is much preferable to lose everything on the alternator side of that fuse rather than lose everything on the battery side of the fuse (the entire electrical system!). So for this reason as well, we want as many of the possible failure points in the alternator circuit (like the shunt in this example) to be on the alternator side of the fuse.
So, where does that leave us with the alternator B-lead circuit:
master relay --> (unavoidable unprotected wire) --> ANL fuse --> (protected wire) --> shunt --> (protected wire) --> alternator
And place the ANL fuse as close as possible to the master relay, to keep the length of the unavoidably unprotected wire between them as short as possible.
Hope this helps.
-Roee