As they should for the business of MLS, and for the better (hopefully). (And they aren't so much "rules or regulations" but merely operational business decisions for and by the league.)
And frankly, I am not so sure this is all that new of a phenomenon other than there is a "name" applied to the process. Technically, every player that goes through the weighted lottery is first signed by MLS without a team assigned. Whether this is structurally different; we may never know. But from a fans perspective on the surface it isn't all that different except that it happens to a non-draft eligible player. Whether this is a new process or the discovery signing process was partially used; it makes no fundamental difference to fans because the discovery signing process was not published anyway.
Maybe to an extent, but if that were completely true then why have we had FO members of both Portland and Philly come out recently and imply confusion about rules, rules the public is also confused about? Tod Durbin says on thing last summer, then Philly FO personnel express confusion/frustration over the same topic only a few months later, strongly implying what was a rule in July was no longer a rule in Jan and that new rules/regulations indeed are not shared or known adequately within the league, whether or not fans are confused. If Jermaine Jones wants to come to MLS in July, do you seriously think every MLS FO has a clear understanding of exactly the process it would take to get him? What about if Altidore wanted to come in July? I think it's highly doubtful every MLS GM would paint a clear picture as well as the exact same picture of the rules/regulations involved to get those two. Looking at a few comments from those within the league over the last year, I think it's tough to argue everyone is clear on the rules, knows the rules and that MLS publicly admitting it makes up the rules as it goes creates an environment where there is confusion, not even taking into account fans and our opinions.