question

You can exclude the default beacon, and then create your own Beacon object.

One thing to be careful of (although perhaps this has been fixed), the location (i.e. altitude) of the light for the beacon object does not respect the scale of the object. The Asobo beacons are quite large (and they don't have a variety of beacon towers like FSX used to have), so when I tried scaling the object, the light was many meters above where it should have been at the top of the tower.

So, what I've done to get around this is to create two beacons, one scaled to proper size but without the light turned on, and one scaled really tiny, so it doesn't show above ground when I set its altitude below the ground so as to put the beacon light at the correct height within the beacon bulb in the first beacon tower, which was set to snap to ground, if you know what I mean.

This is the beacon object I created for KASH when I redid that airport and "moved" the beacon.

<ExclusionRectangle latitudeMinimum="42.77575049786644" latitudeMaximum="42.77620358572847" longitudeMinimum="-71.50822540743619" longitudeMaximum="-71.50756693477194" excludeBeaconObjects="TRUE" excludeEffectObjects="TRUE" excludeLibraryObjects="TRUE" excludeTriggerObjects="TRUE" excludeSimObjects="TRUE"/>

<!--SceneryObject name: RotatingBeacon_Tower-->
<SceneryObject lat="42.77604795822274" lon="-71.50728189557309" alt="0.00000000000000" pitch="0.000000" bank="0.000000" heading="-179.999995" imageComplexity="VERY_SPARSE" altitudeIsAgl="TRUE" snapToGround="TRUE" snapToNormal="FALSE">
<LibraryObject name="{A04B772A-6BBF-4103-B263-D479BCCE71F5}" scale="0.460456"/>
</SceneryObject>
<!--SceneryObject name: RotatingBeacon_Tower (Beacon)-->
<SceneryObject lat="42.77604842384222" lon="-71.50728099818839" alt="-17.00000000000000" pitch="0.000000" bank="0.000000" heading="-179.999995" imageComplexity="VERY_SPARSE" altitudeIsAgl="TRUE" snapToGround="FALSE" snapToNormal="FALSE">
<LibraryObject name="{A04B772A-6BBF-4103-B263-D479BCCE71F5}" scale="0.461100"/>
<AttachedObject attachpointName="" instanceId="{00000000-0000-0000-0000-000000000000}" pitch="0.000000" bank="0.000000" heading="0.000000">
<Beacon type="CIVILIAN" baseType="AIRPORT"/>
</AttachedObject>