We won't know until trial but the confusing bits about this case for me are:
1. Most people, especially LE are aware of the huge numbers of CCTV and ANPR in and around London, impossible to enter and leave London without your vehicle registration number being captured. A hire car doesn't get round this, even false plates aren't fool-proof because the genuine owner of the registration number can be quickly eliminated in an investigation and the movements of the car with false plates are still captured.
2. We haven't heard in the news about the hire car being recovered by the police nor any requests to help to locate it so I guess it was returned to the hire company. Local press / public would usually pick up on this as it would be quite an event if forensics were recovering a car from a company in Dover at the time, maybe the car had been re-hired already to another person so the recovery was kept private. Where was the accused's own car - did he take it to Dover to hire the car and leave it there until returning the hire car.
3. Stranger abductions into car - I've browsed news history, when it does happen in London and other UK cities all seem to have involved a weapon to threaten the individual and the perp usually turns out to have a lengthy criminal history or bad character unless the perp was known to the victim. Only difference here is the possibility of using police ID in the abduction but that wouldn't get the victim 55 miles away without something else happening soon after the abduction.
4. During the missing persons search, it was said that SE's phone signal was last located to a mast near to the site of the alleged abduction. Suggests that the phone was quickly disabled (unless battery just happened to go at that time) and suggests something serious happened during the kidnap or very soon afterwards. A one and a half hour drive from kidnap to where SE was found is unusual for sexual offences that seem to occur very close to the first encounter from reading historic news reports - to much risk of something go wrong / been spotted during the long journey.
5. I'm torn between it being a calculated pre-planned crime vs escalated beyond original intent. The accused had no reason to be where he was or to be in contact with SE so preplanning and bad intentions are likely. However the intent could have been similar to IE that escalated.
6. Builders bag - can see why it was used, easy to carry / drag a body a distance but was it already in the car ready to be used or did he return home for it later? Where was the body during this time if he did? A police officer (Darren McKie) in Manchester killed his wife and left the body in the boot of the car round the corner from his house then waited until his kids were in bed to move her body - the movements of that hire car will be really interesting.