Your question is quite valid, but you are using the word "subdomain" in a not-quite-precise way.
What you are actually asking is about the fact that an Route 53, an A record can give the appearance of referencing either a fully-qualified hostname from another domain, or a hostname or subdomain from its own domain, while in proper DNS, the only way to reference another hostname is with a CNAME, yet those can't be provisioned at the apex of a domain ("example.com") pointing to a subdomain ("www.example.com").
An alias, you're saying, seems to be functionally equivalent but more flexible than a CNAME so is there a difference?
The difference between a CNAME and an alias is that a CNAME is still a proper, standard, ordinary DNS CNAME, which returns a DNS query response "hi, you need to know that the real ("canonical") name of the server you are looking for is 'x'" and, depending on circumstances, may also include the A record for the target host or may not, requiring the client to go for a second lookup.
Aliases, on the other hand, are a clever hack created by Amazon which does not break the protocol yet allows Route 53 to hand out the A record directly from resource "X" when the A record for resource "Y" is requested. Aliases can also reference other record types, but the record type they reference must be the same and for the purposes of this discussion, I am talking about A record aliases.
And, the important take-away here is that an alias actually returns an A record -- not a reference to the target, like a CNAME does.
The catch is that with an alias, you cannot put just any hostname in that box. It has to be a hostname within a domain where Route 53 has the magical hooks so that it can retrieve the apprpriate A record to s
answered 2013-06-20T00:32:22.780