I haven't done any modding, but looking at TWoTS for example, the respective ruleset adding base-defending hunter killers appears to be very simple, most of it caused by making the HKs more difficult as the months pass by:
baseDetectionRange: 600
baseDetectionChance: 45
huntMissionMaxFrequency: 1440
huntMissionWeights:
0: #because no 'firstmonth' can be applied
STR_ALIEN_INTERCEPTION: 100
7:
STR_ALIEN_INTERCEPTION: 100
10:
STR_ALIEN_INTERCEPTION: 90
STR_ALIEN_INTERCEPTION_LATE: 10
14:
STR_ALIEN_INTERCEPTION: 30
STR_ALIEN_INTERCEPTION_LATE: 70
.. and for example STR_ALIEN_INTERCEPTION is:
- type: STR_ALIEN_INTERCEPTION
operationType: 6
raceWeights:
0:
STR_AQUATOID: 25
STR_GILLMAN: 30
STR_NAGA: 25
STR_CARCHARODON: 20
(... omitted some for brevity )
waves:
- ufo: STR_FIGHTER
count: 1
trajectory: P1
timer: 0
hunterKillerPercentage: 100
huntMode: 0 #prefer interceptors
huntBehavior: 1
I suspect adding base defending hunter killers would be a very easy mod, perhaps only a couple of dozen of lines, if you leverage existing missions and ufos to the max. Maybe you could even try to create such a mod yourself.