The engineering world has a maxim called "Murphy's Law", which goes "If anything CAN go wrong, it WILL".
This is not an expression of pessimism. It is an instruction to the engineer, that he MAKES SURE to minimize the number of ways that things could go wrong. Like making electrical plugs intended for different voltages and power levels physically different, so that a plug CAN NOT be placed in a wrong outlet. Like making sure a part CAN NOT be inserted backwards or upside down.
In this case, the engineers failed in their duty to ensure that the wrong type of bolt COULD NOT be mistakenly installed where it wasn't supposed to go.
You have decoded the problem. You are exactly right. We aerospace engineers always specify design differences when possible, to prevent interchangeable parts from being used.
However it is not always possible. Here you have two fasteners with identical sizes and threads. Only the material is different. The design selected should have been the weaker fastener so that a mistake would make the system better. Shame on the engineers in this case if there are places where the stronger fastener is the only one that will work. In these locations, LM needs to fix the product. And I worked for LM. System engineers know what I am talking about.
Probably did it to save money [koff koff] during prototyping and design testing.