It depends on your contraints. We optimized for file download size. By having the database autogenerate, we didn't have to ship an extra db as part of the package.
If you are paying per database fees to your hoster, then combining the two databases into one could save you some money.
From a performance standpoint, merging into one database would be more performant and run a slightly smaller memory footprint. However, you probably wouldn't notice the difference unless you were running thousands of these sites.
As a footnote, this kit isn't meant to be a beacon of performance. We did not excersize certain advanced features and optimizations to make the code easier to understand to a wider audience.
Hope this helps!