Hello Kyle- I just found this thread while dealing with a similar issue- using my jack and jack stands for a front brake job.
I believe these links may help you: (all links safe as per McAfee and AVG site advisors)
Jack pad rubber-coated steel
Jack pad rubber
(first link came from forum in second link)
In another thread, someone had to drill a hole in his floor jack to accept the Eastwood adapter. Not sure if this would compromise the strength of the jack support area.
I think putting the weight of the car on the flanges/pinch weld is asking for bent flanges and a poorly supported car- I believe the pads on the lift in the service manual are meant to seat just inside the flange, but you're right- it's hard to tell.
not sure I understand your question about the sill- I don't know, but I've never seen two tires at once jacked just from the center of the sill with a single jack point- it sounds risky/tippy- however, maybe your floor jack has two contact points, like the one in the service manual.
Also, not sure what kind of tire rotation you are doing that jacking up one side at a time will help- Tire rotation patterns
Also, my all-season Yokohama tires rated for 60K on my AWD RAV now need replacing after 10K more miles than that- all four are worn quite evenly and I only rotated once (but do check tire pressure a couple of times a year). A matter of debate on whether rotation is worth it...Is tire rotation worth it?
Back to the jacking issue: my owner's manual says to use the OEM scissors jack for tire changes under the "front suspension arm rear mounting" and for the rear tires under the "rear suspension arm".
To do my front brake job, I put my hydraulic floor jack under the center of the crossmember (as on diagram in previous post)- there is an indentation in the crossmember there that did not allow a great fit with my jack contact plate- it worked ok, but I will buy a flat adapter (last two links above) or use 1/4" steel plate at this point next time. I lifted from here to raise both front tires just enough to place my jack stands under the front suspension arm rear mountings- my jack stand contact area happened to fit perfectly to these mountings- then lowered car gently onto stands until floor jack was free, but then rose floor jack to just contact crossmember just snug as a safety. Also put removed tires behind jackstands under frame as a second safety. Car seemed very secure (3/4" plywood under jackstands in dirt driveway)- not sure I would yarn on rusted bolts under the car this way...but that's a whole other debate...definitely secure enough for brake job though. According to the service manual diagram above, the suspension arms may be only appropriate for jacking and not jack stands- however, until I order the slotted or deeply grooved adapters for my stands, what I did seemed my only choice...
I am going to try my nice area dealership and writing Toyota re the discrepancy of the jack points from my owner's manual and the service manual above, and also where to get those perfect jack stand pads pictured in the manual- will post if I find anything.
In the meantime, perhaps the Eastwood adapter will work for your floor jack...
I hope there is something here that helps...