From what I understand, the publisher decides what graphic content goes into the books (not the artist or the editor), but of course the editor is the one facilitating the publisher's standard, so the publisher is working through him or her. Japanese companies have dozens of magazines, sort of the way US licensees use different imprints, only on a grander scale. They pick the artist and the magazine and set the standard for graphic content (only in doujinshi, works not made to turn an actual profit or make a living at, leave content totally up to the artist). If the artist knows the standard, or their personal standard is the same as the magazine, there is generally no need for censorship, but if the artist draws whatever she wants anyway, the publisher will censor the drawings, or make the artist do so. This is how we get blurred penises, etc. I would argue it isn't much different from how English publishers set content/graphic restrictions, only they use US standards for "decency" in comics (whether those standards are clearly legal issues or based on general standards of decency that dictate who will agree to sell the product), instead of the Japanese standard, which as we have come to understand from things like the Handley Case, are much more conservative on sexual issues.
On another note, thinking the English companies are doing all of this without the Japanese publishers knowledge or consent is a mistake. The Japanese are very controlling of content, just ask any US anime industry person. The industry is also bigger there than it is here, so they throw their weight around more confidently than a little US licensing company can (and if a licensee were to go against the Japanese licensor's wishes, they could simply refuse to work with that licensee ever again). I'm not saying it happens to all titles all the time, but the Japanese licensors can reserve the right to sign off on all cover art, advertisements, name translations, etc. etc. The list goes on and on. The idea that censorship somehow flies under their radar is absurd.
Even the artist who drew that title that Seven Seas dropped acknowledged that what is acceptable in Japan is not necessarily acceptable in the US. If we want to get our titles printed in English we're just going to have to accept the realities of the publishing world: things like hardcore Shota is not going to get licensed here anytime soon, if ever, and the graphic content of books is going to get toned down in order to spread yaoi to a bigger market. We're not going to see the censorship end until the market is stable and more importantly large enough to support itself without the help of retailers who dictate conservative content standards to the publishers.
You might want to call June "despicable" or "money-grubbing" for wanting to turn a profit, but they are a business, and that is what businesses do in capitalist societies. The artists themselves are "in it for the money," too. They aren't giving their product away for free for the "love" of doing it. They are selling it. Furthermore, DMP, of all the publishers of BL in English, is the only one really stable in these trying economic times (look at Deux, DramaQueen, the closures of Iris, Broccoli, CPM and the recent layoffs at Media Blasters). And I would argue that they are so because they are reaching out to a wider market, and they are doing it by compromising on the "authenticity" of the content.
In conclusion, in regards to referring to June mangas as "bootlegs:" this is incorrect. A bootleg is the illegal production and/or distribution of something. Bootlegging is what scanlators are doing, not what the legitimate business who goes to the trouble of legally acquiring the right to distribute a work of fiction in another language does, regardless of how anyone feels about the "changes" they make. Books being "inauthentic" because they are edited is not the same thing.