It's heavily implied that Perfected Blue Goku (Post-Merus) hadn't reached Jiren's level since it's firmly established that only Moro and UI Omen Goku (Post-Merus) had surpassed the level of the Gods which may include the Hakaishins.
Therefore, if Jiren still remains to be stronger than Perfected Blue Goku by at least a fairly large margin, then the only way Base Goku would have reached Perfected Blue Goku's level from the ToP is if Jiren's power was above A x Perfected Blue Goku where A represents the boost from Base to Perfected Blue. That's very unlikely so Base Goku should get stomped here.