(not OP, but I'll answer this as best I can)
Yes, stages 641-700 (and UX 1-700, etc) are playable with the mod.
1.x.0 versions of Pokemon Shuffle (such as 1.5.0) are downloaded from the eShop, and effectively act as the "base game".
In-between versions like 1.5.1 to 1.5.11 are instead downloaded as "extra data". This also means that deleting your extra data effectively downgrades you to the base game, 1.5.0.
Shuffle's extra data has tamper-protection, so it can't be edited directly. This means, for example, that you can't edit an event competitive stage to be single-player.
However, the base game can be edited no problem.
So what the mod does, is it edits the base game to have all of the stuff from extra data built into it. This also allows for editing the stages themselves, which extra data normally wouldn't allow you to do.
You therefore no longer need the extra data (and keeping the extra data would just confuse the game, as extra tries to override the base). So you delete the extra data, putting you on version 1.5.0.