I think what you have to remind yourself is that Zone 2 needs training also. Whilst in Zone 2 on structured training plan your body is making physiological adaptions to working in that power zone which should gradually bring down your RPE as your FTP increases.
I get the same thing whenever my FTP gets a bump and Zone 2 ceiling rises. Then gradually throughout the year, what was once the ceiling of Zone 2 becomes your lower end and RPE certainly decreases.