Your thought process is on the right track but you're not entirely correct.
Let me preface this by saying that I have only a basic medical/biological education and I haven't bothered to look up anything specific for aluminium with it. This is just going to be on the general process.
Injection and digestion are two different processes and what is a harmful amount in one process is not necessarily a harmful amount in the other.

As an example, there are many venoms that you can safely digest in large amounts, and the specific amounts you need to have venom harmful is usually far larger through digestion than injection. I am not suggesting or condoning any intake of venom through any method.

Your theorising that the 50µg limit is for ingested aluminium may well be true, I don't know. But you are correct that injection and ingestion affect the body differently for the same substance.

However, some substances are indeed worse through direct injection, so " whereas injecting the raw compounds directly into your blood is usually harmless. " is actually incorrect.