Some people think the direct mount setup offers better tone and sustain. I can't say I can tell. I have guitars with both types, with the same woods and same pickups. There is a difference but there are so many small things that can change tone slightly.
I haven't had any issues with my direct mount guitar when it comes to the pickup mount holes wearing out. That may have something to do with the wood. Like basswood is particularly soft compared to mahogany.
I've seen guys having a issues with the trem post inserts egging out in basswood bodies from use over the years, and the wood being soft. So far my 88 540r hasn't had any problems (thank the Lord).
One of the more knowledgeable guys on here Rich, has pointed out to use some CA (high quality super glue) to fix the trem post issue. But I have used your tooth pick fix with something like, strap button screws that won't tighten up anymore. Once you know what you like and have your pickup height right, I would think you wouldn't have to ever touch it again. Unless you have a microphonic pickup or something.