Two Batmen? Basically.
It's hard to retcon in everything as it will never truly work, but essentially Modern Age Batman is the same person as Silver Age batman, just modern age retellings/re-imaginings. The Crisis still "happened" to Batman at some point, and since one Batman is gone, the one that left must be the Batman we're hearing about in Year One… so that means he's Silver Age batman and not Golden Age batman.
The trouble with this stuff is that it takes logic to figure out, but it doesn't truly make sense. So you have to make a call at some point.
You're absolutely right about his Year One stories. It's such a popular setting with fans and creators, so the guy goes through an amazing amount of bullshit in that small set of time. I kind of think the year one era is more like three years, due to how robin comes in and how long some of the individual trades take.
It would be wonderful to have a floppy reading order, but it could only be happen if I was somehow able to make my rent with this. I'm attempting that now, but the trades are a priority and we've got a long way to go. Here's hoping for the future! :D
I'm also thinking that in the future all this stuff will be available online, so it would make it a lot easier to link to the issues through the order for a floppy list. Could be interesting. I hope DC and Marvel gets their act together and realizes how much they could be making my fully digitizing their archives for 99 cents an issue. I'll probably always prefer reading in a bound book, but it would be awesome for research, the odds and ends, and I bet younger generations won't have that preference for paper pages.