The premise of the question is wrong.
Criteria such as charge separation, or charge location, etc are giving a rationale to order the various mesomers in term of their energy.
In the context of VB theory the mesomers (or limiting forms, or canonical f.) are all the possible Lewis structures that one by one cannot describe the actual chemical and physical properties of the molecule. It is understood that none of them corresponds to the actual structure which in turn result by their averaged contribution, i.e. the hybrid of resonance.
"Why is an resonance form with negative and positive formal charges in its atoms, lets say +1 and -1, less stable than an resonance form with just positive or negative formal charges, lets say just +1 or just -1?"
There is no meaning in such an assertion. Beside the use of "less stable" resonant form - in fact it would be better to use an expression such as the less energetic r.f. that as such has an important weight ... ( we have seen that no canonical form is real)...
(I am aware this is common jargon to avoid long sentences but it can be confusing when people are struggling as in the current case),
there cannot be a comparison of two limiting forms with a different number of electrons. If they can be conceived their will be limiting structures of two different hybrids of resonance, in short two different chemical species.`
Note also that a single charge is rather actual and not formal: an ion has that charge whatever distributed.
The OP seems also trying to infer something about the position of acid base equilibrium for which an analysis of resonance effects might be indeed useful to rationalise the behaviour of analogous couples but does not tell about the absolute stability of the participants.
He mentioned in a comment the conjugated couple
Pyruvic acid / pyruvate and try to compare their stability while focusing on their limiting form.
I must admit that the thinking behind it is cryptic to me and that it can be dictated by assuming the wrong assertion above as a rule.
I just point out that the so over emphasised limiting forms with charge separation are formally present in pyruvate as well and made it stronger than acetic acid as for results in an electron withdrawing effect. This are conclusions that can be drawn as mentioned before.
The single minus in pyruvate is not "charge separation in a limiting form" but it IS the charge that an anion must have.