This study of the recently sequenced pine species states that 82% of genome is repetitive. This is characteristic of any complex genome, including humans. Such sequences have often been considered "junk DNA", though any scientist will tell you that just because we don't know its purpose doesn't mean it doesn't have one. That said, a good portion of repeats are due to transposable elements, effectively intracellular parasites, whose only purpose is presumably self-amplification and are more often than not deleterious. These interspersed repeats make up ~45% of the human genome. That paper mentions that, based on sequence homology, ~65% of the pine's genome is made of these repeats (that's 15 billion base pairs).
It's interesting that, even though the pine's genome is ~7 times larger than a human's, it has only twice as many predicted genes. The pine tree has ~50 000 hypothetical genes but only ~16 000 are what the authors call high confidence. When the human genome was first sequenced, there were ~35 000 hypothetical genes but now, some 10 odd years later, there are only ~21 000 predicted genes. It seems too early to compare the two. This also brings up the important point that the number of genes is not necessarily related to organismal complexity: the worm C. elegans has ~20 000 genes.
From the paper:
The large genome size has primarily been attributed to an extensive contribution of interspersed repetitive content (Morse et al. 2009; Kovach et al. 2010; Wegrzyn et al. 2013). Assembly of the Norway spruce genome has shown that LTR retrotransposons in particular are frequently nested within the long introns of some gene families (Nystedt et al. 2013). In addition, there is evidence for gene duplication, pseudogenes, and paralogs, although the extent of these is not clear (Kovach et al. 2010; Pavy et al. 2012).
I have never heard of the hypothesis you mention (not that that means anything), but it seems to me that it's far to early to tell.