Left navigation is the more obvious one. Using the pubslishing left navigation does not provide the adequate nav links for team sites, document libraries etc. in any circumstances. And for this reason only, it is pretty much obligatory to include a foundation master page in each branding solution to be used as the system master, even if team sites etc. are not used in the site collection. The document library views use it! And the settings pages as well, if this has not been turned off in the Web Application settings.
As for the main (global) navigation, it is easier to pass without notice. If a foundation master uses the same global navigation as the publishing master, everything will look just fine as long as the foundation site has been set to use the same navigation as the parent (publishing) site. But if you create, say, a team site not using the parent navigation, you might end up with an empty navigation bar, depending on the navigation setting made in the master page.
So, assuming you use the publishing starter master for the branded publishing masters and foundation starter master for the branded foundation masters, the issue should not even exist. But as the branding work goes, at least I like to create the main masterpage from the scratch and then replicate the master page in order to most efficiently get the page structure copied and then do the alterations for the different purposes, eg. add left navigations to them.
So, if you do it like I do, remember to change the main navigation control as well - or atleast change the foundation master navigation settings to show the current node and display 2 static levels - if there is any probability that the team sites might be used without the full main navigation.