The source of this topic seems to be the condemned 1000 series. Notwithstanding that, let's see whether we can have any take away from that, especially because
MGMAT is has been cited in the discussions on the principles of modification
Following is an excerpt from the Manhattan guide:
1. Right: This model explains all known subatomic particles, SOME OF WHICH WERE only recently discovered.--
The question is whether the second part of this sentence is an IC or just a modifier clause. IMO, \it is an IC since we have a solid subject in 'many of which' and a solid verb in 'were'. The result is that this is rather a comma splice. In addition, the verb 'were' seems to be out of place here, since the first part is in the present tense and a present perfect such as 'have been' would have been better. However, tense may or may not a critical issue here. .
2. Right: This model explains all known subatomic particles, SOME OF THEM only recently discovered.
This seems to be correct since, the second part is a verbless phrase, simply modifying the touching noun 'particles'.
To extrapolate this to the issue at hand,
(D) The mountainous regions of northern Ethiopia are dotted with hundreds of monasteries, MANY OF WHICH ARE chiseled from solid rock centuries ago.
(E) The mountainous regions of northern Ethiopia are dotted with hundreds of monasteries, MANY OF THEM chiseled from solid rock centuries ago
In this also, the choice D is wrong more because D is a comma splice. Of course, whether they are chiseled or were chiseled may not the prima-facie fact.