I think clearly author was using "like it's 1999" as a metaphor, not literally.
It's a fairly common phrase (originating from a Prince song I think) that you can take to mean "like a throwback to a more authentic and possibly prior era." In this case the era is prior the explosion of frameworks and div soup.
Which strangely in this case is not necessarily prior but in parallel, as you said. This is English, it doesn't have to be precise like programming. You can use it for effect.
It's a fairly common phrase (originating from a Prince song I think) that you can take to mean "like a throwback to a more authentic and possibly prior era." In this case the era is prior the explosion of frameworks and div soup.
Which strangely in this case is not necessarily prior but in parallel, as you said. This is English, it doesn't have to be precise like programming. You can use it for effect.