1. Running with weight. Joint considerations have been outlined reasonably above. Do you throw a grenade (or shot put) like you do a baseball? Obviously not. Your rotator cuff would be torn to $hit in short order. Another thing to consider is you don't necessarily want to do something that will significantly alter your form / neuromuscular programming. You can probably get away with a bit of extra weight, maybe 5 or 10 % BW, and still run at 3/4 speed or sprint. But too much of a good thing (like running with a giant parachute behind you or doing overspeed training down a very steep hill), and you are now training a fundamentally different movement, and actually messing up your "normal" running form. To use a more mundane example, consider that when a person has sprained an ankle, they can actually do more long term damage to the (originally) uninjured structures by trying to do "too much / too soon" and then acquiring abnormal compensatory movements (i.e. limping) that may be difficult to shake completely once the ankle has healed.
2. Running with gas mask on. First of all, this isn't really like altitude training.
a) You may be somewhat increasing your "pneumatic resistance" such that the required inspiratory and expiratory pressures are larger (just like in the article quoted). I was involved (actually, as a guinea pig) in research at DRDC utilizing a device called a "Power Lung" which did this in a measurable way. There was no translation to real world performance. The reason for this (I think), is that the lungs are seldom the limiting factor during submaximal or maximal exercise (unless you're a steady smoker with COPD). There are some exceptions to this (e.g. exercise induced arterial hypoexemia), but generally, it's the cardiac output and the rate of utilisation of oxygen by the working muscles that limit performance. Improving the capacity of a non-limiting component is useless.
b) Other than possibly increasing the resistive forces by increasing turbulence / reducing laminar flow, the other probable difference to running with gas masks (vs. without) is that you are increasing "dead space." This means that you are rebreathing the same air to a greater degree. I am unfamiliar with the actual volume of the masks, but if you significantly increased dead space, not only would your breathing mixture be hypoxic, it would also be hypercarbic. This is NOT the same as hypoxic training, which uses a carefully regulated mixture of gas that is hypoxic but NOT hypercarbic. Again, there are a lot of variables (e.g. the amount of dead space, tightness of the mask on the face, rate of metabolism), but the possibility of unpredictably losing consciousness does exist (just like those jokers who hyperventilate before taking a large breath of air and then trying to swim as far as possible underwater).
c) Even if it WAS like altitude training, most proponents of altitude training have long ago adopted the "train low / sleep high" philosophy, because the erythropoietic stimulation of hypoxia can be gained by ~ 16 hours of daily exposure while still having optimal intensity of training in a normoxic environment.
d) The "real world / functional" arguments of the CJIRU-types only applies if you are wearing the rest of your gear. There were people in KAF doing Army Runs and the like with PT gear and a gas mask. I'm no SME on CBRN, but I'm not sure what readiness / MOPP state corresponds to spandex shorts + tank top + gas mask.
Just my $0.02. Well, probably more like 3 or 4 cents, actually. Sorry for the length...
