Like symbionts, obligate endophytic parasites are also coevolved with the host. Does it mean that, do they have the ability and potentially break the chemical and physical barriers of the immune system? and thrive/cause disease to the host.
Yes, what you have said is very right. The obligate parasites have coevolved with their hosts.
The ability of an obligate pathogen to overcome the physical and/or (bio) chemical barrier of the host is closely dependent upon several intrinsic and extrinsic factors. In compatible and susceptible interactions, the obligate parasites almost always overcome the physico-chemical barriers of the host. But, in case of incompatible or resistance interaction between the host and pathogen, there is a localized burst of oxidative enzymes, concentration of toxic metabolites (like quinones, which are oxidized form of phenols) at the site of contact/penetration of the host, reinforcement of the cell wall at the site by increased activity of peroxidase and other enzymes involved in cell wall synthesis, hypersensitive response. These events are followed by an elaborate signal cascade which leads to localized cell death and apoptosis leading to chlorotic lesions.
Hence the ability of the pathogen to overcome the physico-chemical barriers and defense of the host is largely dependent upon the type of host-pathogen interaction, at least in initial stages of disease development.
Though the secondary metabolites provided broad microbicidal activity, its efficacy remaining question to obligate pathogens. The effectiveness of the secondary metabolites may extend to the same species or even belongs genera. Or otherwise, only the particular pathogen of the species/genera may have that ability of resistance.
My assumption regarding incompatible or resistance interaction is pathogens induce chlorotic lesions in the host and leads to die where it absorb nutrients as a saprophytic obligate pathogens.