There are methods of sealing that might make any interior portion "safe". You might be able to use linoleum (but like other plastics it unfortunately off gasses) or you might be able to use a product called marmoleum that is a green building product that is supposedly non-toxic and doesn't off-gas.
Other options would be low VOC wood sealers. Water-based sealers might pose difficulty in that they may not remain sealed if allowed to get wet. It would depend whether the cured form would weaken if exposed to moisture - a real possibility in spilled water bowls or a misted habitat.
I would play it safe and use other woods if possible. Oak, poplar, and other hardwoods are usually cage building safe wood species.
