Its more a case of making sure that house style is followed, silk is not a problem (Being standardised out of the box), but the meaning of the various mechanical layers is not fully defined by the package.
So for example layer Mechanical 20 might be used for example for a milling layer, with 21 used for courtyard, 22 for component centroid, 23 for board outline, and it is kind of important that everyone agrees to do this the same way so that library components all share the same use of the mechanical layers.
Same thing applies to things like default sheet templates and default BOM templates, sometimes to defaults for things like database exports from BOMs to the MRP system.
Agreeing this stuff makes defining a standard output job for a 4/6/8 layer board something you have to faff with once, rather then being something you have to set up for every board for example, and it also makes things like BOM templates and standardised default design rule sets much easier (And Altium, like most of the better systems for non trivial boards, is all about defining design rules correctly).
Same thing with things like library structures and such, but this is actually common to any engineering effort involving more then one person.
You do need to agree this stuff if multiple people are contributing to any project, even an eagle one, even things like default grids for schematic symbols are worth setting a house style for, very boring to find that some clown used a imperial grid when you have your symbols defined on a metric one (Or vice versa).
This stuff is really just coding standards for PCB design and how far you want to take it is just as variable as the level of detail in coding standards is.
If you have never done a project involving a large team you might not see the importance, but it matters when you get more then a very few engineers on a project.
Regards, Dan.