Sorry gm2. I'm an idiot, I shouldn't talk.
I was using the terms too loosely. When I said "scripts" I just meant all the backend stuff. Most of everything in the wp-admin folder, for example. That was lazy and innaccurate, I'm sorry.
I got very long winded, so here's this:
I'm being very long-winded. Here's the very short answer.
If you tweak your index.php and wp-layout.css, when you update, DO NOT over-write them. your changes should remain in place, and at least in my own experience, it is unlikely that the update will "break" anything.
To your second point, I get lots of crawls from google. I use the search engine friendly permalinks, which was easy to set up, but I've heard it crawls well either way.
And now with my useless blabbing...
I'll just explain how I treat the index.php, as I probably should be able to manage to not bungle that. When I made my web page, which is considerably different than what the "default" looks like, I went through and added a lot of traditional html stuff. Div's with text, you name it. I added plenty of static html stuff. They dynamic parts of the page are between the sections of php, which are hard to miss, as they tend to start with <?....
I deleted some of it outright, as it generated html that I didn't need, but mostly left it alone. Now the reason I think you can get away with not updating the script stuff in the index.php is it doesn't really do any heavy lifting, so it seems to be rarely changed.
Mostly I think it references variables or whathaveyou from the other scripts. The php in my index.php is only 10 lines or something, there's just not a lot to fix there. I do get my updates from the CVS, which tell me what files have been changed. If it says the index.php has been changed, I'll look at the php section of index.php that provides the content (the only part I really care about), and if it had changed, I'd just paste over the relatively small section in my index.php. This wouldn't change the look of my page at all, and would take all of ten minutes.
Since I've been using WordPress, which admittedly is only a few months, I've never had to do that. As for the CSS, it makes reference to classes and id's that are sometimes set in the php tags which are in the index.php, which is to say, in an update they could theoretically change those if they wanted, but I don't see why they would, unless it were to add classes or id's that aren't already there. In that case, it wouldn't "break" your formatting.
I haven't had to really do anything to change my wp-layout.css either.