Removing Transform Matrix from the output

No sorry. There is currently no option to create SVG files without transform attributes. You have to postprocess the files, e.g. with Inkscape, to get rid of them. This might lead to bigger files, though.

Aha, Thank you for your answer but i have another question, if i multiply the matrix with x and y with the standard matrix multiplication process, the result X and Y coordinates is correct?

That will probably work in most cases but you have to consider all transformation attributes affecting the current element. For example, there can be transformations applied to a group of elements and further ones to the elements themselves. You have to combine them by multiplication. Furthermore, referenced patterns or gradients can define their own local transformations that must be considered properly too. So it's a pretty complex task to compute all coordinates correctly.