Here is how I look at those two situations:
In Regards To Anchor Text Keyword Percentages And Homepage Link Percentages:
Let's consider how Google probably works when it comes to looking at links:
Even after Google has removed the nofollow links from the link graph they almost certainly take additional steps to determine whether a dofollow link should count or not.
Google probably separates the links that should count (appear natural and trustworthy) from links that shouldn't count (probably unnatural and not trustworthy).
The Penguin algorithm likely deals with the links that fall into that second category, links that are dofollow, but probably unnatural and definitely not trustworthy.
If your website doesn't have any links that Google identifies as (unnatural and untrustworthy) then Penguin doesn't apply to you at all period. So in other words, you might have 100% of your links pointing to your homepage and 100% of them using the exact same anchor text. And you don't get penalized because Google has categorized all your links as acceptable and trustworthy.
So, if a website owner is not out there creating any bad links to their site, then their site is probably going to have very few of those bad links pointing at it. Some might get built automatically from crappy sites like statistic sites and places like that. But if any of those links are dofollow links, they will be very small in number anyway. And if any of those links are nofollow links, those nofollow links don't count anyway so it doesn't matter.
So webmasters/website owners are generally pretty safe acquiring links for their sites as long as they only acquire links that Google is going to trust. That is the magic key to the equation. If Google trusts the links, you need not worry about penalties (in my opinion).
Exceptions or Possible Problems With This Mindset:
What about a situation where a fully legit and useful website has 1,000 pages on it in total and let's say that website has 3,000 inbound links (from different domains) and 100% of those links point to the homepage using the exact same anchor text?
And let's assume that all 3,000 of those links are considered natural and trustworthy by Google using today's standards. Would that site get penalized?
Probably not for a while, maybe never. At least not algorithmically by the existing Google ranking and quality control algorithms.
In my opinion it is very likely that Google uses other (not widely known about in public) algorithm(s) other than Penguin that look at things like anchor text keyword percentages to or percentages of links to homepages or percentages of links to any page on the domain for that matter. I bet they use those algorithms to identify weird patterns and flag websites for manual inspection though. And they probably have some filters that exempt most sites from the algorithm anyway. For example, they probably don't analyze a site with less than 100 inbound links for such things. They would use those types of algorithms to identify patterns that spammers/black hats are using. Then they would improve their existing algorithms to identify those patterns better or maybe produce an entirely new algorithm to neutralize the effectiveness of that rank manipulation tactic.
I think this is why Google warns developers not to use Wordpress plugins and website widgets and things of that nature for link building purposes. They have algorithms in place to identify when someone does that and then they manually decide whether to take action against the person or not. But I think in many of the cases, the existing Google algorithms let those tactics work because the links are from trusted sources. (Maybe they have these things built into Panda by now. I don't know.)
If you are going to build links for your site, don't build any links at all that you think Google would find obviously unnatural and obviously untrustworthy. And certainly don't build any that form a pattern that would be easy for Google to identify with an algorithm. If you only acquire links that Google THINKS are natural and trustworthy, then there isn't much for you to worry about at all.