I think putting this collection of articles together is confusing a number of issues. Generally speaking, almost all engineering industries (microelectroncs, chemical engineering, biotechnology, etc.) are open source. You invent something and you patent it. There is very little trade secret (~= closed source) information in such industries. I strongly doubt that GM crops are "licensed" for use in ways that prevent people from reverse engineering (sequencing) their genomes (unlike the software licenses used by some software companies). In fact I expect that to get approval from various governments you have to provide data regarding exactly what modifications have been made to the genome. What isn't required is that you provide all of the genome sequence data because its currently prohibitively expensive to produce that for each GMO. At some point in the future, when sequencing an entire genome gets cheap enough that it isn't a significant cost relative to producing and gaining approval for the use of a GMO, I expect the approval agencies might require the full genome sequence.

As far as dealing with the cross-pollination issues, the way to ultimately solve the problem is to produce all GM crops using a different genetic code that produces gibberish if it somehow made its way into natural organisms (discussed in more detail here. It will be at least several years, perhaps a decade or more, before we are able to do that unfortunately. Even when we get to that point, it seems likely that the greens will scream that it is unacceptable because using such extensively engineered organisms violates the precautionary principle. What is necessary is to develop guidelines for GMOs that can be considered "generally recognized as safe". At this stage of technology development I can see merit for a guideline that would seek to reduce the chances of the development of superweeds by limiting the herbicide resistance genes used to produce GMOs which are able to cross pollinate with each other.