As discussed in Tunnie's thread, I prefer the roof carrying method.
Much to my wifes annoyance, I have tried three methods.
1. The Thule boot carrier for two bikes = One of the straps came off the boot edge on a bouncy road surface and was dangling loose. I did notice it in time but never trusted it after that. I had to made up special brackets and reverse the hook to make it safer. If you do the straps up too tight it can lift the boot off the seal. The bikes tend to rub against each other as well and it's additional nose weight if towing.
2. Towbar flange mounted for two bikes = Additional rear end weight with an already full boot, especially if you are towing. Pain in the arse if you need to get anything out of the boot or need to hook up a caravan. Again, the bikes tend to rub against each other
3. Roof mounted for up to four bikes = Never had any issues with these. Can be a bit awkward being up high but you get used to it. Wheels are strapped to the channel and the sloping down-tube is clamped. You could put a bit of cloth around the down-tube to minimise scratching. Downside is the height for car parks and ferries but I certainly found this method the least intrusive. Bike direction can be reversed to get four bikes on.
HTH
Regards
Alan