Hi Fea!
Intent is important, and in words like these I personally think as long as you express it, it’s not offensive at all, and is actually very kind. It’s kind of a tricky thing these sort of cases, because most people would just stop at ‘Your English is so good’ and just leave it at that. My personal experience is always the combination of 'your english is so good’ + 'you don’t have the filipino accent at all’ + 'where’d you learn how to speak like that’ which is sort of venturing off into that void of okay this is giving me the 'fresh off the boat’ feel and it turns real uncomfortable, real fast.
Actually, instead of 'you speak english really good’, 'you’re really good with languages’ feels so much more comfortable. Also acknowledges a bi/multi-cultural person’s skill in English, but most importantly, his or her native language/s as well. Wish there was a universal switch on the term, would be nice.