Quote from CorwinI personally wouldn't adjust the portfolio for a single company, just for the fact that you may be applying a different ones at the same time. It's hard to know exactly what the company is going to be interested in based on their ongoing projects etc. so better mention everything in a way that's easy to browse through and get the gist of it (experience with what tools, strong points, extra skills...) and let them cherry-pick what suits them (IMO)
I don't know about cases where employers stop at the cover letter. In my experience, who cares about cover letters? They all sound almost exactly the same, and even when the candidate gets a little original with it, it doesn't stand on its own anyway and can just maybe give you an idea of the personality of the candidate. It could go no further than the resume I guess if the experience on it is way too little compared to the needs for that position, but personally I always click the portfolio link (or LinkedIIn if there's no portfolio) out of curiosity and for the sake of being thorough.
What I meant with this is to create subpages/subdomains eg myportfolio.com/crytek/ or bethesda.myportfolio.com, allowing for different kinds of personalization... mainly like highlighting a project created with the tech a company uses, but of course including all the rest.
I've seen this sort of thing done by some web designers when applying to certain companies they were particularly eager to work with, like creating a resume that looks like an Amazon product page, or writing an in-depth analysis of a product, including the applicant's proposed changes.
Of course is a different market, so just wondering if it sounds too weird to apply or just plain impractical. In terms of time, when you are unemployed or looking for a job, you virtually have all the time you want to spend on these things (of course at the base you want to work building a solid portfolio first).
Interesting insight regarding the second question, I hope there are a lot of people like you in charge of recruiting. If you don't mind I will tag/contact you when I've adjusted some things on my own website to ask some feedback.