What if there were one more question on the installation page, asking for whether comments should be on or off by default?
I think as blog software, having comments on by default is a good choice. If CP is not blog software, like WP is, then a different default may be appropriate.
=== Just for speculation ===
The design choice way back when, to use a table column to hold the comment status, was maybe not the best choice. If the comment status was in post_meta, then it could be assumed to be a global default if it was not present. That default could then change without having to change each individual post. It could also be filtered for each post type. This is why the Discussion settings are so confusing. The one section only applies to new posts, because of how it is stored, but the section on changing it based on time could work either way. You might be able to introduce a new value, like ‘default’, to put into the existing column, and then some logic to get the default (filtered for post type). This would be for leaving the column rather than moving it to post_meta. But there are import/export tools and lots of existing plugins affecting comments that might make it difficult to make either of these design changes.