Among the graphic design basic elements , in addition to the essential ones, typography, color, shape, texture, weight, etc., there's also space: margins, the distance between paragraphs, internal margins in frames, etc.
If any of these elements confer a relevant part to the design and is thus arranged in the project graphic quidelines, altering any of its qualities can be interpreted as a consistency break.
If the tables referred to in the question have as a relevant element in their graphic aesthetics the difference in space between the content of the cell and its frame, something very unusual (image), noticeably altering said precept can generate inconsistency.
If this is not the case, any change in distance that is not exaggerated is not only permissible but may even go unnoticed.
If even so, the change is visibly noticeable, a graphic guideline is not a closed dogma, on the contrary, it's a dynamic element that can incorporate new components according to the evolution of the project or its content.
The visibly more serious problem would be if both tables are on the same page or next to each other. If necessary, add an appendix as a reference in the project guideline stating the difference in content.