Well, it seems that way when the crucial pinch-hit situation comes up, but that doesn't mean it actually is that way over a full season. There aren't really that many good pinch-hitters in the entire league. Or in history. The current Phillies bench should actually be a strength in this regard given that all these guys will now play a bit more than they previously would have, which keeps you sharper for the days you don't.
In the DH era I just don't see it. The Phillies' bullpen issue isn't that the starters go long (which is a good thing!), it's that they are carrying two long relievers and almost never use one of them.
And Thomson probably has very little say in that particular roster decision (even aside from Turbull and Ruiz being stuck on the roster). There's no way the GM and analytics people think it's an issue.