These kind of junctions exist. If navigation tools provide the wrong instructions, then the issue lies with those tools.

You are just taking those which sit really close together, but you can't solve cases like this one without severely disrupting the layout of the ways:

https://osm.org/go/0GVMEvoGr?m=

(And you'd anger a lot of mappers if you did.)

TomTom could look at https://wiki.openstreetmap.org/wiki/Proposal:Junction%3Dintersection instead, and consider using that to collapse several nodes into a single logical intersection. But it really shouldn't be necessary to change anything. Just collapse the intersection in the navigation model if the distance falls below a certain threshold.