To answer on your first question, Google doesn't read this as France or Germany, but that doesn't mean it is bad for your SEO.

For example, having those different subdirectories in one domain can help you get lots of backlinks to one domain instead of backlinks to all your location based domains.

To answer your second question, your URL doesn't do all of your SEO work... If you use the right title tags, urls, on-page elements you can rank with your .com domain for different languages.

Yesterday I analysed a webshop that targets different countries (FR, NL, DE, ENG) but doesn't have different domains for each country and I must say that he was ranking for some competitive terms in several languages. If your overall SEO elements are good to target a certain language or country it doesn't matter that much if it is a .fr or .com/fr

Bought the SEO Spyglass of SEO Powersuite like 3 months ago and it's a great kickstart for linkbuilding research. I didn't try the other tools in the suite, but if they are as handy to use like Spyglass it's worth every penny.One of the reasons I like their software is also their pricing, it's not recurring so you just buy it once and I'm sure you'll get the ROI soon!