"f a speaker was designed to operate with a port, how can it be correct to plug the port, thereby making it a virtually sealed box? "
Plugging the port is an extreme case.
The effective approach is to restrict the air flow through the port to various degrees in order to reduce the energy level at the low frequencies the port is designed to enhance to various degrees as well, more or less like a specialized type of bass tone control.
Good speakers are designed to perform well in a variety of rooms however the room acoustics largely determine the results regarding the bass region to which ports are directed. Obstructing the port to some degree (as opposed to blocking it which is the extreme case) can be looked at as a way to fine tune the design of the speaker to best match the room. This does not defeat the design in any way if done right, it merely adapts it better to the room and teh listeners location within it. Its another (easy and practical) thing that can be done to better match the speaker to the listener's environment, along with tweaking speaker location and toe-in, room treatments, etc.
I would say it is ill advised for anybody to be spending money on upgrading equipment until they have done everything they can first to optimize the sound of what they have in the listener's environment. That is the key to good sound in most cases. Obstructing the port to various degrees is just one weapon in your arsenal if your speakers are ported.
Rather than follow some dogma about what is the right and wrong way to approach audiophile sound, try tweaks like this that are easy and cheap to implement and painlessly reversible as well if needed and let your own ears be the judge, which is all that matters.