That is an excellent question.
A little more insight into the difference between the upper and lower mounting bolts: I once ventured into a part of the manual that I had never looked at before, and your query reminded me that this section may reveal some further information. So I delved back in there and had a look. It sure does:
In the General information section, it describes the various characteristics of key fasteners - and in the Rear Wheel Suspension section, it lists the two nut and bolts for the upper and lower suspension fittings.
The size and torque are the same for both, but in the remarks colum, it says NOTE 6 for the upper, and NOTE 5 for the lower.
So you then go hunting for what Notes 5 and 6 mean.
A couple of pages earlier is an easy to miss list, headed NOTE:
5. U-Nut
6. ALOC bolt/screw:replace with a new one.
So there we have it, all perfectly clear.
You can then go hunting for ALOC and U-Nut.
Google search reveals the most likely explanation -
A Fujilock Unut is one of those nuts that has a stainless steel spring device on the outside thread, to help prevent the nut from turning.
ALOC is anybody's guess as to what it stands for. Google searches reveal only opinions, and the dealers that I have asked don't know either - but every ALOC bolt that I have seen from Honda has a thread locking compound already applied to the bolt threads. But that is a fairly limited sample size.
I have never undone either of these two bolts, but just by looking at the manual, if the bolts are employing two different locking mechanisms as would appear to be the case, and they are both the same size thread (the general info quotes 10mm for both) - then I wonder if it is possible to re-fit the bolts and accidentally switch the nuts - ie make the error of fitting the U-Lock nut to the upper ALOC bolt. This would leave the lower mounting bolt with no thread locking mechanism to prevent the nut/bolt from turning.
And have I just solved the alleged Pan / ST1300 weave issue?
[edit]From another Google search, it appears that ALOC is now a registered trade mark of Bowers and it seems to relate to 'metal fasteners, namely quarter turn fasteners'. This trademark appears to have been filed in 2009. So when my manual was written in around 2002/2004, I guess that the term ALOC was not a registered trade mark. Whatever - it means something different now, and I just hope that no-one goes buying a quarter turn fastener to hold their brake calipers and rear suspension in place !
I wonder if there are any Honda shop manuals that are published after 2009, and what terms they use for these 'ALOC bolts'. [/edit]