It would seem to me that you should start by thinking very hard what type of job you'd enjoy - are you going to prefer making marketing stuff with photoshop, or making website layouts or coding the behind-the-scenes javascript for webpages, or the C# that sits behind that?
Rather than thinking "Microsoft is so huge, I'll never be able to fit in", you should think "Microsoft is so huge, that there's a 99% chance that what I want to do is encompassed by some part of Microsoft". It's not that Microsoft is so huge that you can't fit in - it's that it's so huge that there's lots of room for you to fit in.
With regards to whether Microsoft cares that you have PHP - they (to my knowledge) don't have any PHP positions, but they _do_ have lots of PHP programmers - that is to say programmers who can, or even actively do program in PHP. By having a basis in PHP you are saying to Microsoft that you are a programmer who _can_ program in PHP, and this tells them that you can program in languages like PHP, and think through problems simmilar to those that you encounter on a day-to-day basis with PHP, and it's that more than the PHP that is important to Microsoft.
With regards to whether Microsoft cares that you can code in a standards compliant way - they probably don't massively care so long as it works (for proof, right click, view-source), but that doesn't mean it's not worth anything to Microsoft. by saying you conform to the standards means that you're the type of person who would conform to standards - you're not the type of person to use cheap short-term hacks in order to get round a problem and leave the mess for the future.
Supposing you were coming to me for an interview and you came into my office and you said the things you said in the first paragraph, I would have my doubts about you - not because you're a weak candidate, but because you don't seem to believe in yourself, and you're starting with the assumption that you won't fit in. If you challenge these assumptions and say to yourself, "hell - I have YEARS of programming experience, hell I can code AND I can design, and there's not many people who can do both. More than that, I'm basically cheating on my interview by watching C9 videos, because I can regurgitate them in an interview and sound incredibly smart about various bits of Microsoft, how could they not hire me", then chances are you'll find it's a self-fulfilling prophecy.