For the OP: I think you might be hung up on the assumption that your kid will have to become fluent in conversational Hebrew, which is not true. Many frum people in America can easily learn a sefer written in Hebrew, but could not carry a conversation with an Israeli (myself included). It’s not because there are massive differences between modern Hebrew and the Hebrew used in sforim. It’s more because visual comprehension of a language can be easier than audible.
That being said, there ARE massive differences between Biblical Hebrew and Hebrew used in later sforim. I think most would agree that Biblical Hebrew is significantly harder. As the result of your kid’s age and this program you’re discussing, Biblical Hebrew seems to be the main focus right now, but that’s not because it’s the logical, language-comprehension starting point. He might continue to struggle with memorizing pesukim and their meanings for a long time, but that doesn’t mean you should worry that he’ll struggle to understand written Hebrew for the rest of his life.