Am not aware of any detrimental uni-chassis consequences of making access holes in the locations I think I understand you to have described. However, I am not into automotive chassis/body work to give you structural advice. That said, I would think that should any of those sections develope holes from crap inside, and the exterior areas merging into rotting rust holes.., what are you going to lose, or not lose?
On the driver's side of my '89, the floorpan was rotted away mostly from the body/door side, towards the tranny hump, and towards the slope area up to the firewall, and back towards the seat bolting rails. Ripped that area out, and replaced with a sheet of steel roughly, etc., to restore it. One thing I noticed was the interior of the frame rails, and noticed that the inner surface was somewhat involved in the rust zone due to the aforementioned. I used OSPHO, a watery light blue/green liquid of straight phosphoric acid, (danger Will Robinson), and used a recycled spray bottle to squirt all areas of rust, before rebuilding. It makes rust into an inert rust oxide. (The product you are looking at contains the acid as part of a receipe. I'm willing to divide such an all-in-one application, for the actual separate ingredients into several steps instead, i.e., no blending required; gaining complete dispersion of each, and complete coverage).
I'm real cautious with the stuff, so I suggest to those who have never used it before to wear sacrificial clothes, gloves, mask, and goggles, as it will eat them, and you. Depending on what results you want, usually three coats, (3 days), are necessary, with descaling involved inbetween steps, and then a primer paint, paint, etc. However in the area you are describing I would consider that after you flush out the rails, to also follow it up with a blast of OSPHO. J.C.Witney used to offer, and may still, a spray trigger/buttun handle thing costing perhaps twenty bucks. It permits you to connect it to an air hose via one port, and then another port allows you to connect a vinyl hose, say a four footer. This hose can go into any stable container, containing any liquid. When you trigger the button, air pressure goes through towards the nozzle end, sucking/picking up the fluid through the hose, and out the nozzle. The spray is forceful enough to run through, and completely coat the interior frame rails, i.e., stick nozzle in one end, and it will blow out the other hole you make, and any other holes already existing.
I've used the JCW spray rig to CLEAN grease, etc., from engine compartments, engines, trannys, etc., using GASOLINE, (which has it's dangers of course), but as a solvent, does a great job because of the greater air pressure, greater flow, over a hand-held recycled spray bottle. Not sure I'd want to use the JCW rig to do the complete underbody surfaces with OSPHO, though.., I'd stick to the recycled spray bottle, with appropriate protective clothing, etc.
What I did; EXAMPLE: With vehicle up on jack stands, a drop-light, etc., Brush, Scrape away all crap, rust, etc., and then from underneath, lying down, starting at one end, spray everything with the little bottle, working, (pulling, sliding one's-self), towards the other, thusly avoiding drips, and most splash-back. Next day, do the same thing in the opposite direction. That's about 1.5 coats. Let dry another day. Several Rattle Can Primers, allow to dry, and then several rattle cans of rust preventative paint. From then on it's mostly just a one rattle can of paint once a year. It's easy! 1,2,3, parts, and 1,2,3, days. Consider marine grade paints.
