Shouldn't be an issue. Each time I've done this, I've been on different airlines and tickets (and even different alliances) going in and out. Sometimes I was asked for proof of onward or return travel at check-in. Sometimes I wasn't even asked at check-in and my boarding passes had "DOCS OK". For immigration, I think the only place I actually had to show proof of my onward/return travel at immigration was in China when I used Transit Without Visa and they wanted to verify my onward flight did indeed qualify for TWOV. I admit I've never done this in HKG so YMMV there on whether they ask at immigration, but in terms of meeting entry/exit requirements, this should be a non-issue as you have proof of onward/return travel.

The one thing I will note, and it doesn't sound like an issue in this case since unless there's some nuance not known, since you're already planning to enter HKG on the outbound (unsure about the return) is when you do this on back-to-back but separate tickets, you need to ensure you're eligible to enter the country of each destination on the ticket, even if you don't actually plan to enter, because this will matter to the airline. This came up in the Delta forum a while ago where someone was denied boarding to JNB because even though they had a separate ticket onward to a different country in Africa on South African Airways and the person did not intend to enter South Africa (clear customs/immigration) at JNB due to the onward "connection" (put in quotes because as far as DL was concerned it wasn't a "connection"), they did not actually have the proper documents to enter South Africa, which was their final destination as far as DL was concerned, and thus were denied boarding by DL in the United States. So something to keep in mind if you ever plan such a transfer. I.e. while it seems like it shouldn't be an issue, if on your return you're planning to to do MNL-HKG on CX then not cross through customs and immigration into HKG on the return and instead simply "connect" to your AC flight, you will still need to verify you could otherwise actually enter HKG on the return (passport validity, etc.) since this is not a true "connection" as far as the airline taking you to HKG is concerned.