The IBJJF specifically bans1 two judo-throws where uke lands on their head/neck. Despite the IJF prohibiting throws which "may endanger or injure the opponent especially the opponent’s neck or spinal vertebrae", there are a number of throws where it is not uncommon5 in competition for uke to hit the mat first with their head, or impact with it after falling, and which seem to fall under another clause in the IJF's rules where 'involuntarily' impacting the mat with uke's head does not incur a penalty for either party.2
As such, theoretically the set of legal judo techniques appears to be a subset of the set of legal BJJ techniques, but in practice the following two throws are permitted in judo even with uke impacting the mat with their neck/head:
Prohibited: ... Suplex takedown technique, landing with the opponent’s head or neck on the ground.
The use of this technique is still permitted provided that the movement does not force the opponent’s head or neck into the ground.
Hikikomi-gaeshi when used to defend against a single leg takedown (sukui-nage, kibisu-gaeshi, kuchiki-taoshi) is illegal in BJJ if the uke lands on their head:
Prohibited: ... Grab the opponents belt and throws him to the floor on his head when defending a single leg situation while his opponents head is on the outside of his body.
While leg grabs are no longer legal in judo under IJF rules, the counter hikikomi-gaeshi itself can still be performed.
1. IBJJF Rule Book - 6.3.2 Technical Fouls (Version 4.0, Feb. 2015)
Special attention will be given to situations where tori attempts to throw his opponent during tachi-waza with, for example, seoi-otoshi (drop seoi-nage), sodetsurikomi-goshi with the grip on both sleeves and koshi-guruma with both grips on the collar and uke makes an involuntary head defence. These are examples and this situation can occur with other throwing techniques. In this situation there is no penalty for either tori or uke.
• Sport and Organization Rules of the IJF (version 13 October 2018) (p.123, 2.)
• Explanatory guide of the judo refereeing rules (9 March 2018) (p.17-21)
3. Note: there are two groups of similar throws often called "Khabarelli". One, where tori grabs and lifts uke's leg in addition to the belt (obi-tori-gaeshi, no longer legal under IJF rules), and one where the leg is not grabbed (hikikomi-gaeshi, similar to sumi-gaeshi with a belt grip)4.
4. Kodokan Judo: Throwing Techniques (p.218-223)
5. Ura nage compilation video (times: 0.27, 0.42, 1.05, 2.36, 3.32, 3.52)