I bought from Japan years ago and it was problem free very fast delivery from what I recall I do think that the current situation has thrown buying many things from abroad into a bit of a hassle.
I recently purchased from outside the UK (Germany) the price advertised was not including VAT so that was paid on arrival, basically the delivery company handled all that I got an e-mail to say my parcel had arrived the VAT was so much and how to pay it. I paid the VAT and the next day the parcel was delivered. From what I recall there was a charge (Cant recall how much perhaps 20 for admin) Obviously prior to Brexit this problem didnt exist so it was a lot easier to buy from Europe and a lot of dealers in Europe seemed to have JDM watches so it avoided all this hassle of worrying about import charges.
The other issue you have to factor in is getting the watch serviced, I know you mention if there is a problem but you should also think about what happens when its service or repair time? I know for GS they can be sent through Seiko UK but having a poor experience with them in the past not sure I would be happy sending a watch off through them and taking my chances everything will be ok.
The biggest problem I find is the different rates different countries have and as you say, some companies include the local VAT in their price or on other occasions I have found even when their local VAT is taken off the price still seems off (Presumably they have to factor in their own admin charges when they are selling to you)
Re Chrono24 prices I dont know what JDM watches you are looking at but have you looked at Watches of Mayfair? A while back I was curious about a few Grand Seiko watches and found prices on Chrono 24 were worse than on WOM once you factored in the import charges. A google of some of the watches also came up with up to 20% discount. I just gave up in the end couldnt be bothered with all the hassle.