I know what you mean. I don't like putting toms on snare stands, because I can't ever get it close enough to the center of the bass drum, which is what I prefer.
There are alternative rail mounts as well. DW's is actually really good (and surprisingly affordable) and also Gibraltar makes one too.
Another alternative would be to use the Ludwig Atlas Arch mount. You replace two lugs on the bass drum and the rail mount runs off of those two lugs. The replacement lugs have an adjustable hole pattern, so it's once size fits all. On the plus side, you get the rail mount you want with no drilling at all. On the minus side, those replacement lugs are pretty bulky (and can be difficult to fit into a case properly) and it is pretty pricey. You can also use an additional Ludwig Atlas mount that replaces the lug on your tom as well (and as shown in photo 2 below), so you can have a suspension or isolation mount without the (thoroughly modern) look of a typical suspension mount.
Also, for a mere $20, DW offers a claw hook clamp that mounts on the wood hoops of your bass drum. It can mount anywhere that there isn't a lug in the way. Most people use it for cowbells, splash cymbals etc., but you can use it to mount a drum too, as shown in the photo below.
It's up to you. They are your drums. I would least explore the DW Claw Hook/Atlas Arch mount first, just so that drilling is a last resort.
The first two pictures are the Ludwig Atlas Arch, the third is the DW rail, the fourth is the Gibraltar rail and the fifth is the DW Claw Hook/L-Rod combo, shown holding a snare drum.
V