A There are many Midrashim that were around then that are not not around anymore. If Targum Yonasan was composed or compiled during the Rishonim period, the author drew from these same Medrashim.
B Until benignuman provides a reason to assume Targum Yonasan was not written by Yonasan ben Uziel don’t assume it.
C Here is the reason to assume it is not written by Yonosan ben Uziel…
Haleivi- Even if you would be able to speculate about the timetable of the origin of the Targum Yonasan, and were able to say that ‘Targum Yonasan’ ‘drew from Midrashim’, the fact that many of Rashi’s statements have no other known source than the Targum Yonasan, still allows for the possibility that Rashi used the ‘Targum Yonasan’ which itself would have ‘drawn from Midrashim’, and that Rashi didn’t himself draw from those Midrashim.
benignuman- This possibility would in turn invalidate your argument that Rashi never saw Targum Yonasan, which would in turn invalidate your inference from there.
And again, there is definitely nothing to be ‘wary’ of.