If you take the laptop with you in your travels, it's very easy to scratch the screen with the keys, because the laptop is always next to other things in the bag or backpack that causes the pressure on the display surface to increase, hence making the inside part unkindly touch the keyboard.
On the other hand, if you only use the MacBook at home you might not have the same issue.
I've dragged MacBooks in my travels domestically and internationally, with them just tossed in my bag, and never had a screen issue either.
Not saying some do, but it doesn't appear to be widespread.
This means you annoy half of your users by not letting them charge in the direction they’re used to,
I suspect they'd simply get used to it, it's not like charging only one way is an earth shattering event; even so I suspect Apple could engineer a magnet on one side of the iPad and a pencil like the current layout of one on each end to allow dual pencil positioning and a landscape camera setup if they wanted.
as well as make the pencil less stable when it’s attached.
True, but it's not exactly stable currently unless the iPad is on a surface and not moved. The whole idea of magnets as a way to keep it attached when not in use but in a bag etc. needs work.
Of course the power users who want to do all their Mac heavy lifting on the iPad are going to quickly encounter the thermal throttling joys of a thin, sealed device with no vents (even the MacBook Air has vents in the hinge) and a heat generating screen on one surface.
Considering the iPad is not really sold as a power user's replacement for a powerful Mac I suspect most users don't run into this issue even as they do real work on it.