Doubt: Why are actions belonging to PP and PMC not arranged in logical sequence?

But I have a doubt: If these actions are to be performed in that specific sequence, why is the left panel not designed accordingly?

Starting guide present one of the many ways to do thinks.
It is some help for newcomers that would not understand how to start.
Many experienced users will not refer to it.
And I'm sure you'll notrespect this sequence when you'll have the habit to use ProjeQtOr.
(Morevor, creation of resources should be done only once, then you'll only add new resources, so you'll use this menu not very often)

The project allocation is in Environmental parameters > Allocation to projects menu.

It is one of the ways to do this, and the the most used one .
The most used : you create a project, then you allocate resouces from project view
Or you create new resource, and you allocate it to project from resource view !

The assignment of activities is in the Follow up > Planning menu.

Not only.
It is done on activities that can be reached through "activity" menu.