STOP!
Do not do anything until you at least read what I am about to tell you. I am in no way an expert or claim to have all the answers but I have done this several times and I can tell you what works and what does not, and what will absolutely lead to more work. Then, proceed as you see fit.
Ironically, I just received the replacement tank for my GS1100ET Tuesday by way of a good eBay deal. Last night, yes, Christmas eve, I started in on this exact project... removal of the tacky, circa 1970's/80's, badges, smooth tank indentations, etc.
Proposed Method 1) tap down below level surface, if necessary, and simply fill with polyester filler, a.k.a. Bondo, Rage, etc.
I have done this once. Although it will look fine for 1 or 2 seasons, eventually it will crack or separate or both from the metal badge bracket/tab. The thermal expansion/contraction rates of the tank metal and of the polyester filler is different. Over time, the tiny pockets of air underneath the bracket and the Bondo will allow separation. It will! One day you will look down at it and see a perfectly traced outline of the tab showing through the paint or the paint itself will also be cracked in this pattern. It will ruin your day, pi$$ you off, make you wish you would have read the rest of this post. I had this day once... OK, more than once.
Proposed Method 2) use epoxy the same way as method 1.
Although I think this would be stronger and last for longer, It will eventually suffer from the same fate, depending on the type of epoxy used of course. However, the main reason to avoid this method is that you won't be able to shape the epoxy with a sanding board or by hand sanding very easily. One of the characteristics of polyester fillers the way they are cut away by sand paper and ability to be sanded at a rate comparable to the paint and primer surfaces you are working with. Epoxy is just not a good substitute. Besides, Bondo has a catalyst type reaction when mixed properly, and provides you a material you can shape into the curve of the surrounding area perfectly. For the record, I have had this day as well.
Proposed Method 3) Break away the tab via prying or lifting tabs off.
This WILL leave holes in the tank where the spot welds were. I have done this, bad idea, tears the metal right open and you now have holes in what was a sealed tank. BAD! Now you get to weld closed a gas tank. (not actually as bad as it sounds, but a pain in the ass none the less)
Proposed Method 4) Approved and known to work. Grind away at the spot welds, remove tabs gently, trying very hard not to tear away the metal and leave holes in tank, remove the rust that is going to be under the tabs in most cases and then fill with polyester filler of your choice. Which, with no rust and air pockets will properly adhere to the metal and if done correctly, last as long as the paint job you put over it.
This is where I am now on this very project.
Note the rust I still need to remove. I got the easy to reach rust already but the deeper indentations have to be cleaned out with smaller sand paper pieces which I have not done yet.
Now the bad news. Even grinding carefully can burn through the spot welds. The hole I made shown here, now gets to be welded. I will get pics and write that up when I do that too. It's not as hard or dangerous as people make it out to be. I have welded on 3 motorcycle fuel tanks and all had gasoline in them just hours before the welding took place. Just have to clean them out a bit first. I will post more on that when I do it. Plus the rest of this process if you guys want to see it that is?