I reread the BMM p.41 and TW p.122 sections dealing with this. The wording is a little different, but the end result is going to be the same.
Let’s take a look at a COM-2D Commando that takes a Gauss Rifle hit to the Left Torso (15 damage vs. 6 armor, 6 structure).
Following the BMM steps, we have:
1. DOES THE LOCATION/FACING HAVE ARMOR?
Yes; spend 6 of the 15 incoming damage ticking off the armor pips. Go to Step 2.
2. IS THERE DAMAGE REMAINING?
Yes; 6 more damage is applied, ticking off the structure pips. Go to Step 3.
3. DOES ANY INTERNAL STRUCTURE REMAIN IN THE LOCATION?
No; go to Step 5.
5. ARE THERE EXPLOSIVE COMPONENTS IN THE LOCATION?
Yes; roll to determine crits, and see if any tag the ammo bin. If yes, resolve the explosion (2 Pilot hits plus probably fatal ammo explosion damage). If no, go to Step 6.
6. IS THERE DAMAGE REMAINING?
Yes; go to Step 7.
7. DID THE DAMAGE RESULT FROM AN AMMUNITION (OR OTHER INTERNAL COMPONENT) EXPLOSION?
No; transfer the remaining damage to the CT and return to Step 1.
Also note, now that the LT is destroyed, the torso destruction rules on BMM p. 45 apply. Further hits in this phase that strike the LT (or LA) will automatically transfer towards the CT.
Following the TW p.122 steps:
1. Does the location have armor?
Yes; apply 6 of the 15 damage ticking off the pips.
2. Is there damage remaining?
Yes; go to step 3.
3. Does the location have an internal structure?
Yes; spend 6 more damage ticking off the pips. Go to Step 4.
4. At the beginning of the current phase, did the location contain any components that could sustain a critical hit?
Yes; roll Determining Critical Hits and apply. Go to Step 5.
5. Does any internal structure remain in the location?
No; all crits and remaining armor are destroyed without exploding. Go to step 6.
6. Is there damage remaining?
Yes; go to Step 7.
7. Did the damage result from an ammunition (or other internal component) explosion?
No; the remaining 3 damage transfers to the CT and the process repeats from step 1.
I think the confusion is in the wording of TW steps 4 and 5. You will have checked for and resolved any crits (including possible explosions) before getting to step 5, where everything in the destroyed section is crit out (without detonating).