Throw out the notion of Google "clicking" on a link. This makes no sense as a concept. Google will crawl a page and take all of the links found on that page and put them into a database. If a site has never been visited, these links are put into the queue to be crawled. If Google already knows about a link, then it goes through another process.
Google will index each page based upon how fresh a page is. If a page updates often, over time Google will revisit the page more often and up date the index more often. This can be as little as just a few minutes or it can be as long as a year or more.
If your home page is redirected and Google makes a request for a page that is redirected, it will follow the redirect. If if is a 301 redirect to another domain name, you may be confusing Google. I am not sure what the effect should/would be exactly. However, I am sure that it will not effect any other page and how that page performs. But it will effect the home page. However, if you are doing a 302 redirect, the confusion may not occur. A 301 redirect is a permanent redirect whereas a 302 is redirect is a temporary redirect. I would advise a 302 redirect over a 301 redirect. In the case of the 301 redirect, you are in effect saying your home page is now over here and that you should remember this.
Your example code, is defaulting to a 301 redirect. If you were to use [R=302,L], then I suspect that no SERP performance change will occur as a result.
