Baking – Bagels: Flat, no rise, gumthe inside. Over kneading

You are spot-on: Whole-grain recipes often use more water and tend to "flow", so using a loaf pan is typically the way to go. Loaf pans alow for a "wetter" dough.

It is absolutely possible to bake a free-form whole-wheat loaf, but it needs experience with kneading, resting time and shaping to balance the water content and comparatively low gluten. Also, for the final rise you had better not rest it on the counter, but in a floured basket (in a pinch, a bowl will do) to avoid the "flattening" effect you noticed. Bake in a very hot, well-preheated oven on a hot pizza stone or in a hot dutch oven to encourage proper crust formation and a good oven spring in a humid environment. (Unless you are going for the solid "Pumpernickel" type, but that would be in a loaf pan anyway.)

So find another recipe (or experiment yourself if you have the experience) and you are good to go. I have successfully worked with high water content (up to 80%), but always with a poolish/pre-fermentation with a long slow rise to "soften" the whole-wheat and get the enzymes going. Doing a few rounds of stretch-and-fold during the first rise helps to align and strengthen the gluten structures (and a tablespoon or two of additional gluten ("vital wheat gluten") is a good trick up your baker's sleeve as well...). Sourdough is optional if you are baking wheat-only, but if you use rye, you should definitively look into that subject as well.

If your main goal isn't a whole-grain loaf, use a classic "Artisan bread"-type recipe, and start exchanging some of the white bread flour with equal parts of whole wheat flour (and - optionally - add some gluten). Find your personal ratio where the result satisfies you. For 20-30% whole-wheat you won't notice much of a difference, with 50% your loaf will get denser and possibly need some "tweaking", e.g. a splash of extra water. The "long-cold-rise-with-very-little-yeast"-types are the most flexible in my experience.

(The oil isn't a problem.)

Ok, this is going to be a long post, so patience, please.

1. Ratios and gluten
   Your dough has a pretty mainstream ingredient list, meaning average hydration and a rather high yeast content. Whith the whole wheat you could go a notch wetter, but that is a question for another day.
   As you are not using any slow-raise / stretch-and-fold method, you need to develop your gluten by mechanical kneading. A few minutes in a machine sounds like the minimum of time, not like overkneading. Go by the appearance of the dough: It should go from lumpy to homogenous to very smooth, or at least mostly so if your whole wheat is very coarse. (How to handle this would be another question.) Only after that stage would you get to "overknead" and the dough tears. An overkneaded dough would have serious trouble rising at all, because the glutem strands are torn and can't hold the CO2.

2. Timing
   I'm actually surprised that your dough is even willing and able to rise after a six hour first raise. My gut feeling, reading your ratios and with regard to the fact that you put the bowl in warm water, would be one hour maximum for the first rise. Whether such a fast rise is desirable is again another question. The general rule with yeast is to use visual clues, not a timer. Unless your recipe states otherwise, go for

   first raise = double volume.

   As I am currently baking, let me share a few photos:

   
   (Please ignore the bad quality, I had originally snapped the first photo only as visual reminder for me...)

   This is also true for the second rise:

   

   Ideally you want to bake your bread when it's slightly underproofed to maximize oven spring. Oven spring is not only a funny show to watch, but it means a light and fluffy loaf.

   If you greatly exceed raising times, two things will happen: First, your yeast will be "spent", loosing the ability to "lift" your dough, second, the gluten structure that you created while kneading, can weaken, causing the dough to fall flat.

3. Tension
   When shaping your loaf, you want to keep the gas bubbles mainly intact. This does not mean that you can't touch the dough, just that you shouldn't knead in the sense of "mixing thoroughly" (there are exceptions).
   What you do want, though, is a taut surface of your loaf: Just like with a balloon, this will help your loaf to expand in all directions instead of flowing outwards. You are not destroing gluten here, but actually using it.

   There are many techniques, most are either based on a round "ball" which can then be pushed into a longish loaf, if desired, or start with a "roulade" of dough. The latter is typically used for baguette.

   For a boule (round loaf):

   

   First fold the dough towards the middle or slightly off-center (above: after three folds) until the surface (= the underside) of the loaf is taut. Then turn it over and rotate the loaf a few times on a non-floured surface, pressing the edges "down and under" with the edge of your hand.

   For a baguette:

   

   First gently flatten the dough in a somewhat rectangular shape. Pull the far end up and push hard with all ten fingers down to seal. Repeat until all dough is rolled up. Hold your thumb parallel to the long axis and pull the dough over your thumb towards you. Work your way along the loaf, creating mainly crosswise tension. Roll gently to smooth out and shape the edges.

   Normally I use this only for real baguette, which is way thinner than the loaf here, but for the sake of a better explanation, I used the "baguette technique".

4. Tools
   Note that I am using two different bannetons here - basically because I have them and because I can maneuver the loaves easily. If you look at the photos of the second proofing, you will notice that the loaves are quite "stable" per se. For (softer) baguette, a couche or, in a pinch, a floured linnen towel helps keeping them in shape. Place the baguettes between raised folds like I did with these breakfast buns: