Yes - you use washers. Just one needed at the rear, because a pop rivet already has a rim. This is a common technique. Pick a light rivet and it won't compress the plastic much. For the handle bolts I use a little 4mm spacer, as the web page shows.
I use these for EeZeBilts, which are typically light - but the biggest one I have carries nearly 20kg, with spare batteries and radio and everything inside. A kid can sit on them - indeed, I have done so on occasions. You use the 4mm thickness, but if you really want to use them as seats you would probably be better off with 6mm. Of course, if you wish you can build a wooden frame inside if you want to carry something really heavy.
What I like is the cost. You can get 5 sheets of 8ftx4ft on ebay for less than £50 - that's £10 per sheet with free delivery. If you go to your nearest stockist (look for 'twinflute') and carry them away they will probably be £5 per sheet. And you can typically get 4 boxes out of a sheet.
The cost of a strap handle and some clasps is minimal (a few quid on ebay), so you are looking at a custom-sized box for a fiver or less. Means that you can box ALL your boats at low cost, and then stack them away under beds or out in the shed. I must have a dozen or so of these piled on top of each other... and they are very light, so you are not carrying any extra weight apart from the boat...
Incidentally, I've standardised on these toggle clips - they seem to work the best...
https://www.ebay.co.uk/itm/Case-Box-Stainless-Steel-Spring-Loaded-Toggle-Latch-Catch-Clip-6pcs-Y6U9/323801617239?hash=item4b64149357:g:3S0AAOSwhMJc004r