Right now the cesium writer has a somewhat cryptic approach to writing tiles. Roughly speaking, it tries to build the tiles dynamically, filling them one feature at a time. If a feature is too far away, it starts a new tile for that feature. It keeps filling the tiles with 'close' features until it reaches the max feature per tile number. One of the problems is that it does this in geocentric coordinates. That is why the bboxes of the tile look like they are jutting through the earth's surface at odd angles, depending on the latitude.

We recently implemented an I3S writer and in this process developed more of a quad and oct tree approach to writing 3d tiles which we are working to optimize. Once we are happy with the I3S writer, we plan on revising the Cesium writer to make use of these lessons. In the mean time you can try reducing the number of features that you write per tile, as set by the writer parameter. You could also try computing the centroid of every feature and then sorting your features by the x and y of that centroid. That might make it easier for the writer to group features closer together.