There two important things to note.

1. If the same genetic programme leads to two phenotypes because of the environment, this falls in the category of epigenetics. Epigenetic processes are usually not tree-like, hence, poorly modelled by inferring a tree.

2. You implicitly assume (via your R-script) that homoiologies (in a strict sense, i.e. parallelism) are rare and not beneficial (neutral). But if the homoiology is beneficial (i.e. positively selected for), it will be much more common in a clade of close relatives than the primitive phenotype (the symplesiomorphy). We can further assume that beneficial homoiologies will accumulate in the most-derived, advanced, specialised taxa, in the worst case (from the mainstream cladistic viewpoint) mimicking or even outcompeting synapomorphies. A simply thought example: let's say we have a monophylum (fide Hennig) with two sublineages, each sublineage defined by a single synapormorphy. Both sublineages radiate and invade in parallel a new niche (geographically separated from each other) and fix (evolve) a set of homoiologies in adaptation to that new niche. The members of both sublineages with the homoiologies will be resolved as one clade, a pseudo-monophylum, supported by the homoiologies as pseudo-synapomorphies. And the actual synapomorphies will be resolved as plesiomorphies or autapomorphies.

Without molecular (and sometime even with, many molecular trees are based on plastid in plants and mitochondria in animals, and both are maternally inherited, hence, geographically controlled) or ontological-physiological control it will be impossible to make a call what is derived (hence a potential homoiology) and what ancestral in a group of organisms sharing a relative recent common origin and a still similiar genetic programme.