I think if you’re wanting to be clear in your speech, you’d put more emphasis on the fact it’s two words (the teacher at the class I go to kinda does that: rising intonation on the “ja”, small pause, then falling intonation on the “arimasen”; not limited to that one word, she just does that generally when she wants to be clear or put emphasis on some point). Plus there’s just difference in the way different people say things – I’d probably side with the native speaker than Koichi, just since he’s not native, you know?