So I figured out that you can create, delete, and modify objects without using the console. You can even get achievements without it detecting cheats!

Commands like "ent_create portal_weight_box" and "sv_portal_placement_never_fail 1" can be executed through binding them to a key.
Almost every command that doesn't require sv_cheats can run this way.

To use the bind command (if you don't know how:
bind "key" "command"

Example:
bind "c" "ch_createairboat"

Unfortunately, some things, like spawning energy pellets, noclip, and godmode require sv_cheats to be 1. You can't get achievements with these.
Still, this makes beating the challenge maps MUCH easier.

Hope this helps!