The application of tile to the existing wall sounds fine. It would be rare to install backerboard here because the drywall is an adequate substrate, and the surface is not subject to much moisture. It saves time and money and as long as the (not glossy) surface holds the mastic or thinset is what I would do. As far as tiles not being flush...flush with what? It doesn't sound like professional workmanship from your description.
Using particleboard for a laminate counter can be done, but my preference is to use exterior rated products that stands up better to moisture. That said, most commercial fre-fabicated counter is in fact particleboard. ACX or better plywood or engineered laminate substrate is expensive, so that explains why a lot of particleboard is used instead at about 1/4 the cost.
Particle board is very absorbant. It drinks water and glue. If the laminate counter was fabricated on site, the particle board should have been sealed or multiple contact cement coats applied. The first coat seals and supports the second coat, and the second cement coat would actually hold down the laminate, which would also be glued.
Most likely, only one coat of contact cement was used and it was absorbed into the particleboard causing an inadeaquate bond. This has progressed to delamination and the washboard effect. It is also possible the particleboard could be taking up moisture near the sink area if the sink is not adequately sealed, but this would be noticed in a more localized area. Can't prove it, but that is what it sounds like.