Yes, you can have custom build sites and sxa sites in the same Sitecore.
The answere from Sitecore on this question:
Can you mix SXA and non-SXA websites within a single Sitecore instance?
is a bit more nuanced
Yes (and no). The challenges of mixing SXA with other solutions are the same as with running any two solutions from different implementers on a single Sitecore instance. Non-SXA sites and SXA sites share pipelines, and both attempt to add processors and modify Sitecore behavior to its needs.
SXA did extensive reviews of all pipelines within recent releases. We have made sure we abort our processors whenever we detect that they are running outside of the context of SXA sites, for the very purpose of limiting any interference that SXA could cause for another solution.
We have tested it working with the Habitat and confirmed that they could run side by side. SXA should be as unobtrusive as any Sitecore solution can be to another solution.
On the other hand, SXA is not in control of the behavior of the processors from the other solution - which means the cohabiting code also needs to be a good neighbor and check for interference with SXA’s operation if it is to be deployed to the instance that co-hosts SXA.