David,
As innocent by-standers, we do not know why the person "up the chain" said no detection was required. Also we have no justification from you, other than that the standard says so, as to why the detection is required.
If, for example, there is no reasonably foreseeable location and type of fire that could lead to smoke entering the lantern light without, en route, activating one of the installed beam detectors, then what would be the point of detection in the lantern light? In this case I would suggest that all parties could safely agree to the variation.
On the other hand, if it is foreseeable that a fire could start in a location that would fill the lantern light with smoke without activating the installed beam detectors then we have to consider this: Does it matter? That is to say, this scenario would indicate that there is a delay in the actuation of the fire alarm system (presumably the smoke will descend, eventually, to reach the beam detectors). This delay in actuation is very likely to have negative consequences on the fire safety provisions in the building but only someone with a full knowledge of the fire strategy can know this.
So I would suggest that you ask yourself: 1) Is there a foreseeable location and type of fire that will not be detected by the installed beam detection? 2) If so, would a delay in alarm actuation have a significant effect on the fire safety provisions in the building?
If you feel that fire safety is not compromised then the variation can be agreed; if you feel that fire safety is compromised then all parties cannot agree to the variation and the certificate cannot be signed to say the the system complies with the standard. In other words, if all parties cannot agree then the system cannot comply with the BS. In other, other words, if the standard is to comply then all parties must agree.
Stu