I don't find Lama Surya's article at all difficult to understand. Actually, I think it is cogent and well written for the audience He's writing for. I think He's making two main points:
1. Tibetan Buddhism is not a monolithic theocracy, although it may look that way to the uninitiated from the outside. Students (even when they become Teachers in their own right) are responsible really only to their direct Teacher(s). If a student goes rogue and no longer follows the commands of their Teacher, they're pretty much on their own to do as they will until the law of karma, cause and effect/action and fruit, catches up with them. Do not expect the TB hierarchy to denounce Geshe Roach. It's just not gonna happen. They don't operate that way. Should they operate that way is another question, and a good one, but that's a different discussion. In my experience, Tibetan Lamas do not make negative pronouncements about other Lamas in public, regardless of what they may say about those same Lamas in private.
2. The practices of TB can be dangerous and especially to those who are mentally/emotionally unstable. This is one reason the Guru-disciple relationship is so important. The Guru is supposed to check out the student just as carefully as the student is supposed to check out the Teacher. Only when the Teacher believes the student is ready are certain practices given or allowed. At least that's the way it's supposed to be. We all know about the metaphor of the snake in the bamboo tube, but, foolishly, most of us don't think that applies to us. Bottom line, Vajrayana is the fast path, but is also the dangerous path, and "fools rush in where angels fear to tread." Obviously, Lama Surya is not gonna say exactly those things in His Huffington Post blog, but I believe that's what He'd say to you or me.
Further, unfortunately, even if the student has thoroughly vetted the Teacher, there is the possibility of the Teacher going over the edge. The Teacher going bonkers and leading His/Her students astray is one of the very real dangers of the Vajrayana. Chatral Rinpoche's wife/consort is the daughter of a famous mid 20th century Terton. This Lama had a vision of a bay-yul (hidden land) in the snow mountains. He told His students that they should follow Him to this bay-yul. Somewhere between 80-150 of this Lama's most devoted students sold all their worldly possessions and set off with their Lama to find this bay-yul. Their first attempt, they were turned back by some circumstances (I forget exactly what; a snow storm or something). So, after making further preparations, they tried again and were never heard from again. Some people, including some Lamas I have talked to, believe they were all swept to their deaths by an avalanche. Others believe this Guru and His chelas entered the hidden land and are residing there now. Those Lamas I've talked to who think this Teacher led His students astray do not criticize the students for any lack of perspicacity on their part. They use this story to drive home how dangerous the Vajrayana is. Honestly, to some extent it's a crap shoot and all depends on karma.
Sure, as organized, risk-averse Westerners (sorry, I'm presuming you're a Westerner), we would like to see a very neat and orderly hierarchy which polices itself and acts as a safeguard. But that's not the way this system currently operates. Further, ask yourself if you really think a highly organized hierarchy like the Catholic Church would do any better. Historically, think of the Inquisition. More contemporaneously, think of the priest-pedophile scandals. Bottom line, samsara is dangerous.
Pema Chophel པདྨ་ཆོས་འཕེལ