With this is not critical at all, it's a good case exposing how there is some stuff, update_shipped_tours() for example, that can end being called multiple time in different steps of a component upgrade.php
This is about see which alternatives are, and decide how to handle these cases in general, documenting it and, in particular, fixing the update_shipped_tours() case.
There are various alternatives:
A - Allow code to happen unconditionally out from upgrade savepoints. So arbitrary code can be executed and the beginning or the end.
B - Achieve the arbitrary code execution by supporting my some new post-upgrade php script (similar to install.php).
C - Build some mechanishm within the called code, so it' sonly executed once.
D - Simply, remove the old calls, keeping always the last one.
And that's all. Feel free to add more alternatives or comment about any of them.