The total force on a charge is equal to $\mathbf {F}=q\mathbf {(E+ v×B)}$ where everything have their usual meanings . We can say that:
$$dW= \mathbf {F\cdot dl} = {\mathbf{F}\cdot \frac{d \mathbf{l} }{dt}} dt= \mathbf {(F\cdot v)}dt = q(\mathbf {E\cdot v})dt = \mathbf {(E\cdot j)} dt ...... $$
where $\mathbf {j}$ is the current density vector created by the charge and it is non zero only at the point of point charge. [...]
You're assuming above that $\mathbf E$ above is not the total field, but only that part of the total field that acts on the charged particle. This is correct in point particle theories a la Tetrode, Fokker, Frenkel, Feynman-Wheeler, but it is not the usual meaning of the symbol $\mathbf E$; the usual meaning is that this is total field, and that all charged particles are spatially extended bodies, with finite (or regular enough) charge density everywhere, so one total field $\mathbf E$ can be used in all equations, and then density expressions in the Poynting theorem are all finite and can be interpreted in terms of energy.
Now from Maxwell's laws:
$$\mathbf {j}= \frac{1}{\mu}\mathbf {\nabla×B} -\epsilon \frac{d\mathbf {\tilde E}}{dt}$$ where $\epsilon$ and $\mu$ are electric and magnetic permittivities. We have to note here that $\mathbf {\tilde E}$ is the total electric field, not only the electric field which acts on the charge .
Actually, this is not necessary, because Maxwell's equations (with appropriate source terms) hold for each and every component of EM field defined by its source, and also for total field and total (sum of ) sources. So it is quite possible to write down the above equation only for that part of total electric field which acts on the point particle.
But let's assume $\tilde{\mathbf E}$ in the above equation is the total field.
Thus $\mathbf {E}$ and $\mathbf {\tilde E}$ are not same. But in Poynting's theorem both are treated same and thus dot produced with $\mathbf {j}$. So is the theorem wrong?
In the Poynting theorem (for charges in vacuum), total fields $\tilde{\mathbf E},\tilde{\mathbf B}$ are used only. Thus the term $\tilde{\mathbf E}\cdot\mathbf j$ in the Poynting theorem involves total fields $\tilde{\mathbf E}$ and $\mathbf j$.
This is mathematically invalid in case of point particles, because the field is too singular at the particle, so the product $\tilde{\mathbf E}\cdot \mathbf j$ is undefined (meaning, its integral is undefined). So for point particles, the Poynting theorem has singular points, and cannot be interpreted in terms of work/energy. One has to formulate different (but mathematically similar) local conservation law, without singular points. This is possible using adjunct fields (one distinct field for each particle) and then that theorem, with defined expressions that have finite integrals, can be interpreted in terms of work and energy.