Sure there is a reason: Many applications, alias analysis in particular, only use a subset of Datalog. Subsetting languages very often makes for easier and more efficient implementation. If you know that there is no negation in your alias problems, your special purpose solver can be much more efficient than a Datalog solver that must be prepared to deal with negation.
Of course you might wish for a generic Datalog solver that you could run in a special mode where you promise that it will not encounter negation in the problem you give it. But that is then no longer a Datalog solver but a "well engineered purpose built solver".
As for the "built in" part, anything that is not built in must cross an API boundary and usually translate between different data representations. That is a theoretical reason for being slower.