Also, the two chambers are not equal. The Senate is very clearly the upper chamber.

The House is the chamber with actual power, while the Senate was intended to act as a check on the House and the executive. That's why the 17th amendment made such a mess: they were supposed to represent state interests, and especially having a balanced budget is much more a state interest than a popular interest.

In particular, for any bill requiring spending, the Senate can only amend a bill that started in the House. Impeachment must start in the house and is then tried in the Senate. The Senate can't nominate someone to office, they can only confirm a nominee presented by the executive.

Spatial metaphors are not illustrative. Please give some examples of what you mean.

This isn't a spatial metaphor any more than "upperclassmen" and "underclassmen" are for high schools or "left" and "right" are for politics. We call it the "upper" chamber because it's supposed to be the higher status, more "dignified" chamber.

Words have histories of course, and probably at one point this was a spatial metaphor - maybe some bicameral legislature literally did have one of their higher status body on a different floor than their lower status body. But the words upper and lower when applied to the legislative branch have evolved since then.

The Senate alone has the power to confirm every judge in the entire judicial branch. The House has absolutely no say in any of that.

The Senate is who convicts impeached officials. They approve judges and cabinet appointments.

All states get at least one House member.

Should some states have zero?

No, but the total number should not have been fixed in 1929 to stop continued increase (and thereby accelerate inequality in representation.)