The folklore article in a sibling comment to yours clarifies it a bit. Apple did make their own, but it wasn't running on the Apple ][ or compatible with what was running on it. That was still their biggest revenue stream, and they couldn't afford MS withholding a license for BASIC on it or fragmenting the community (two versions of BASIC on the same platform depending on date of purchase). So they made a pragmatic choice to avoid getting screwed by MS, who went and did what they always did (especially back then): screwed them anyways.

Simply starting a credible project to do their own could have cause Microsoft to soften its terms.

As for a different version of BASIC, nothing stopped Apple from making a work-a-like BASIC. After all, that's how the Compaq was made, and plenty of other work-a-likes.

From a modern point of view, the software in those days looks pretty simple. I'm surprised there weren't a lot more clones.

I can only take the folklore article as accurate here, but it seems that it boiled down to timing and cost. They probably could've done it, but their existing BASIC project had already taken a couple years. If they'd elected to replace MS's BASIC implementation with their own, they'd have had a year or so to get it done. And failure would've been very costly.

Corporate risk tolerance comes into play at that point.