So I decided to call Sony today to confirm a few of my questions. I was surprised how fast I was able to speak with a live operator, took only about 30 seconds of waiting.
Sony confirmed that they will still provide service to users who have opened their PS3 units, so long as EVERYTHING is exactly where it's supposed to be. Meaning that if you forgot to put back that tiny screw that's semi-hidden beneath the power supply they won't touch your machine. Now that's probably an extreme case but they stressed to me that any type of MODIFICATION of the PS3 will result in a service denial. Keep a detailed track of where everything goes if you decide to open your console.
Their service fee is $149 plus any applicable state and local taxes. This fee covers everything. So say your PS3 has a bad motherboard, blu-ray drive and hard drive. The price will still be the same, so no worries.
Keep in mind that they will still erase your hard drive so use the backup function if you plan on keeping those game saves.