The main idea is to plot whole number metrics (such as number of conversions) and rate metrics (such as conversion rate) on 2 different axes, see Conversions and Conversion Rate on different axes.
Rate metrics should be visually identifiable using the % symbol and rounded to the nearest whole number.
Since 3013 it is possible to specify which metrics should be plotted with the columns parameter.
Here is how multiple axes should be handled at the API level :
Metrics can be identified using their name as rate metrics should always contain the term 'rate' : strpos($name, '_rate'), probably refactored in Piwik::isMetricPercentage().
Requires #3831 for automatic inclusion of multiple axes in scheduled reports.
Attachment: Conversions and Conversion Rate on different axes
Linking example image