The following tests fail with root layer scrolling enabled:
http/tests/devtools/tracing/timeline-paint/layer-tree.js
http/tests/devtools/tracing/timeline-paint/paint-profiler-update.js
http/tests/devtools/tracing/timeline-paint/timeline-paint-and-multiple-style-invalidations.js
http/tests/devtools/tracing/timeline-paint/timeline-paint-with-layout-invalidations-on-deleted-node.js
http/tests/devtools/tracing/timeline-paint/timeline-paint-with-layout-invalidations.js
http/tests/devtools/tracing/timeline-paint/timeline-paint-with-style-recalc-invalidations.js
http/tests/devtools/tracing/timeline-paint/timeline-paint.js

The basic idea of invalidation tracking is that trace events (e.g., the devtools.timeline.invalidationTracking trace event in Node::SetNeedsStyleRecalc) are recorded for all invalidations and paints. These events are then connected together in devtools/front_end/timeline_model/TimelineModel.js. For example, a style recalc event that precedes a paint will be considered an invalidating event for that paint.

There is an issue with the LayoutView with root layer scrolling enabled because invalidations are issued with the LayoutView id but the paints occur with the scrolling contents layer id and we do not correctly associate the invalidations with the resulting paint.

I think we may have a similar bug with all composited overflow scroll areas. I wasn't able to see where this is broken in the devtools UI so this may not be user-visible.