When a creator creates something, they acquire an implied copyright that gives them 100% control of how that creation is distributed. To add to that the MyTrainz Agreement recognizes that copyright to be valid and binding and requires all users to respect the rights of the creator as a condition of use of any service offered by N3V Games.
With regard to the use of the label "freeware" as an attempt to suggest that a creator that allows users to download their creation(s) from their website or from the DLS for free is somehow the same as the creator relinquishing their 100% control of how their creation is distributed is a false assumption. Unless the creator specifically gives users the right to redistribute their copyrighted content either on the their website or in the config.txt file of the asset, that right is not granted by downloading their copyrighted content.
Now we come to web archiving services. You are of the opinion that what they do is legal but yet there are at this moment thousands of copyright infringement lawsuits making their way through court systems all over the world. So clearly not everyone agrees with your opinion. In the case of The Internet Archive which is the parent organization of the web archive, they claim that they have the altruistic purpose of preserving the content of the Internet for future generations. They further claim that they are doing no financial damage to the copyright holders since what they are preserving was made available at no cost in the first place. And as well, they claim no copyright over the content they are preserving and are providing free access to said content. So it seems on the face of the matter that you might have a point. What they are doing might be legal. But the plaintiffs insist on pursuing legal action anyway. Why? It seems to me that their arguments are based on two ideas. First, it was their choice at the time to distribute some of their content for free for a promotional benefit to themselves. For example, JR and RRMods both offer older content on their sites as free downloads to attract people to their sites in hope of converting them to paying customers. From time to time, some of that older content is removed due to it no longer being consider of high enough quality to serve this purpose. The second argument is that a creation that once had low value now has a higher value and by it being distributed by the archive, the creator is denied the exclusive right to profit from it. An example would be a young writer that published short stories on a blog before being discovered and offered a book deal to publish the short stories as a book. The writer takes down the short stories from the blog but the archive continues to distribute the stories without permission. In the Trainz world, this could be seen as a creator choosing to start making payware based upon their older freeware which they rework and update to payware quality. In doing so they removed the older content from the website. RRMods chose to replace the old site with new sites that did not have the older assets available for download. That is their right. The web archive has no right to continue to make the old stuff available to anyone without the creator's permission. Recently, I saw that The Erecting Hall was granted permission to update and release some of the older RRMods content. That is the proper way to do things.