I recently got my 1971 RT1B running after it sat in my garage for several years.   I bought a new Parts Unlimited 6N2-2A-3 battery which worked fine until I saw battery acid running down my chain guard.  I mixed up some baking soda and water solution and poured it on everything I thought the acid may have touched.   My first thought was that I had bought a leaky battery but after further consideration, I thought the battery may be too tall and the seat pan was hitting it when I sat on the seat.  To check this, I put a couple of dabs of grease on the seat pan, and a strip of newspaper on top of the battery and then I sat on the seat.  The newspaper stuck to the seat pan. 

 I checked some threads on this forum and found that people had the following solutions:  1,  Buy a sealed Motobatt MBT6N4 ($37) battery which they used with the larger DT3 battery box.  2.  Buy a Power Sonic PS640F sealed lead acid battery (which is much cheaper at only $12.99.  3.  Buy a Yuasa 6N2-2A-3 battery standard wet battery (about $40 delivered without acid).   The problem I found with these solutions is that all the batteries are still too tall.   My Parts Unlimited battery is 3.75 inches tall, the motobatt is 3.8 inches tall, the Power Sonic is 3.94 inches, and the Yuasa is 3.75 inches, the same as my parts unlimited.   I thought that the DT3 battery box may compensate for the additional height but I have one and it actually made the situation worse.  The raised mounting tabs on the RT1 box allow the battery to sit lower in the frame than the tabs on the DT3 box which are attached flush with the top of the battery box. 

 I thought about modifying the battery box by extending the bottom but there is only about 1/8 inch clearance between the bottom of the box and the rear fender.  I tried removing the rubber grommets from the battery box and the battery still sits too high.  I noted that the battery strap tab at the front of the box is higher than the battery but also noticed that there is about a 1-1/2 inch wide recess in the seat pan to accommodate the tab.  The recess is not wide enough for a 2.76 inch wide battery.   There is a wider recess which I believe is supposed to accommodate the battery but still doesn't provide sufficient clearance height for the 6N2-2A-3 battery.  

It seems that other people have successfully applied the three solutions listed above but I wonder if their seat pans are actually hitting their batteries, but the batteries are holding up and not leaking.  One other thing I thought of was that maybe the original OEM battery was not as tall as any of the ones listed.  i tried to find the brand and model for the OEM battery and the closest thing I found was a Partzilla RT1 parts diagram picture where it shows a GS MV1-SD battery which I believe was a Yuasa.   I couldn't find a current listing for that model battery.  If anyone has one, I would appreciate them checking the height.  I would also appreciate anyone offering their thoughts on the issue.  Obviously, there are a lot of RT1Bs and DT1Es out there still running around with batteries so maybe my problem is a screw loose in the driver.      

I've experimented with several options including what you mentioned. The Yuasa 6N2-2A-3 fits correctly with proper clearance of the seat with everything else stock.
For the MotoBatt 6N4 with a '73 battery box I have a thin pad on the bottom of the box and thin pad on the seat. On one of the boxes I had to file small notches on the sides to clear the wires.
On one of my '71 DT1E I have the Power Sonic PS 640 F1. Its 3/8 of an inch taller. No retainer bracket across the top of the box. Thin pad in the bottom of the box. Vinyl tape on the bottom of the seat. Heat shrink tubing on the spade connectors I made. No clearance issues. 

I've seen some seat pans pretty much loose their structural integrity and "collapse"...  they tend to rust from the hidden (and allegedly never painted) top (foam) side of the pan.

Ditto on what mark said. Plus the rubber pads on the seat pan can deteriorate or be missing. Check that you have all 5 in place.

I checked and found I have all 5 rubber pads although three of them have some permanent compression.  I'll see if I can find some replacements.   I checked the seat pan for any obvious cracks but did not find any.    I have a replacement seat foam coming in so I'll be able to check the top of the seat pan when I install it.  I pulled the thick foam from the battery of my battery box and replaced it with a thin pad.  I also trimmed the rubber mounting grommets so they are not so thick.  I ordered a Miady Sealed Lead Acid battery (SLA 6V5a) which is similar to the Power Sonic battery but slightly shorter at 3,86 inches high (vs 3.94 inches).  I've used SLA batteries in my YM1 and YDS3 bikes and I'm amazed at how long they last.