I've always been of the opinion that the map comes last. The map will be based on many variables, many of which can be affected by changing engine parts, even if they are only minor bolt-on parts. Now I appreciate that they may only make a tiny difference, but it's a difference none the less.
I'm no mechanic so I'm not for one second going to argue with somebody obviously more clued up than me. But I personally would prefer to know the map I'm getting - assuming we're talking custom here - is based around the exact setup of my engine and related items. Even minor changes can have an affect so I'd personally want it to be as accurate as possible.
I would have been of that opinion myself, but having had "custom" maps on heavily modded cars in the past, I feel qualified to say that a "generic" map can work better.
Don't forget, the ECU is always adjusting, start off with a custom mapped car and with a generic one, then drive for 1000 miles and they would have both adapted.
Why do you think the custom one would have adapted more than the generic one?
What do you think needs to be adjusted on the custom one anyway?