The obvious solution to me would be to fly it QNH using the altitudes from the FMS which can be cross-checked with the chart, rounding cleared altitudes to the nearest 100ft. QFE only procedures are becoming less common but we used to do this all the time.
Even if changing FMS approach procedures is not prohibited outright, it's not a good idea as it increases the chance of errors manifold. Sooner or later someone is going to flip a number and cross a fix 900ft too low. Some A/C don't even allow tinkering with STARs and approaches.