Using different applications for different plots is not uncommon, especially when there are collaborations among different groups which are accustomed to different applications.
For instance, I have a number of papers published with various groups across the world. I'm used to plotting graphs by using the workflow Matlab->matlab2tikz, whereas other coauthors of mine are more confident with Origin. For diagrams, I usually work with Inkscape, but other groups may have other preferences.
Most of the time, we didn't have any issue, but there have been rare occasions in which a reviewer (you know, that reviewer #2, the nitpicking one) asked us to make the diagrams more uniform across a paper. This request was typically not referred to plots but to circuit diagrams, and it was more related to the symbols used rather than the diagramssoftware used, but indeed it's easier to guarantee uniformity when the same software is used (in cases like this one, when I'm the first author, I usually volunteer to redraw everything in a uniform way with the same software).