Can I use Per-Title encoding together with SSAI?

Yes, that is possible!

SSAI providers are usually encoding the ads to a pre-defined set of resolutions and bitrates which is quite static. Changes in resolution are problematic, changes in bitrate not so much. That is why you can just configure the Per-Title encoding to restrict the possible resolutions to a set that is provided by the SSAI provider. The configuration works in the same way as configuring required resolutions for your Per-Title encoding.