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For internal linking you should try to be as precise as possible. You can also freely control the anchor text of the links so if you're talking about a specific product, link to that specific product. Google has enough data to know when you link to a page and the content it should be finding is not there (as may be the case with some of your home page links).  I would clean up any and all internal links that don't point to the best page, either deleting ones that just don't apply or pointing them to very specific products. With external links it can vary. A lot of times people link to the home page when mentioning the company, while some sites garner a lot of product specific links (eBay, Amazon, Craigslist, etc.) due to the nature of their content. Wikipedia would be another example. Using OSE you can find some great ideas around how the competition has built links, but also some really spammy examples. Avoid the spam and make it a goal that when you do add a link to a page or work with someone interested in linking to your site, that the link is as user helpful as possible.  Think of the link or mention from a conversion perspective more than as a way to help your rankings and you'll be much better off. Cheers!

Ryan is absolutely right, Enhanced Link Attribution doesn't come even close to creating a problem for your SEO. It won't generate any URLs so you techie might be confusing this with another feature/ tool.

Then I wouldn't mess with a .co unless you wanted to buy up all the TLDs for you brand name. For instance, if I were HP, then I would get HP.co for trademark reasons.