I can't speak for carlaa, but a previous post stated that since coffee contains phytoestrogens, it should be avoided since the phytoestrogens in coffee would compete with those in PM. The phytoestrogen levels in coffee are extremely low in comparison to PM so it is very unlikely to have much if any negative effect on PM at the cellular level. Again, at the risk of putting words in carlaa's mouth, I bet she would say any negative effect someone saw with moderate coffee consumption and PM would have much, much more to do with the quality (low) of the PM than the coffee consumption.
As far as the article link you posted, unfortunately more recent research has demonstrated coffee to have a protective effect as far as breast cancer goes and seems to promote metabolization of estrogen in women of certain genotypes. One of the studies below didn't find increased risk from coffee consumption until it exceeded 8 cups/day!
http://www.ncbi.nlm.nih.gov/pubmed/16978896
http://www.ncbi.nlm.nih.gov/pubmed/9511854
http://www.ncbi.nlm.nih.gov/pubmed/16365077
http://www.ncbi.nlm.nih.gov/pubmed/19775332
The study you cited said coffee may increase estradiol levels in women (probably won't find the same relationship in men since we don't have ovaries to produce estrogen, and increased FSH levels in men have a different effect than in women) but apparently there are other factors involved since coffee also seems to have a protective effect as far as breast cancer is concerned. The general conservative opinion is that anything with estrogenic effect increases the risk of breast cancer. And yet, above are recent studies showing a protective effect from coffee, while studies from Thailand and the far east show PM to have a similar protective effect as far as breast cancer is concerned. Apparently the protective effects persists despite coffee inducing increased estrogen production in women and the very high estrogenic effects of PM.
Several things need to be kept in mind, research studies such as those you posted and the ones above, NEVER show cause and effect. Thus, drawing a conclusion such as coffee increases estrogen in women, therefore coffee is bad for women with endometriosis, is at best flawed. Also, from the myriad research studies done on coffee, there are obviously other mitigating factors/substances in PM and coffee or associated with caffeine containing beverages that complicate the matter. Unfortunately, it is just not a black and white situation.