I think that no matter how you wanna do it, be sure to secure the probe, and make sure to factor out possible temperature changes, like urates. You could do this by isolating the probe, or do daily checks. Either way, have a method of security and daily monitoring.

The reason why I think it doesn’t really matter how aside from what I’ve just stated, is because your thermostat can change settings! If it’s outside the enclosure you’ll have to set it around 96 to get it to 90 inside the enclosure(for example). If your probe is inside then you set it to 92, so that you can get 90 above the substrate(for example).

I think choice of where to put the probe is based on personal choice. Above the substrate is risky but maybe you have a way to secure it and check on it regularly so that it’s being monitored, and have been able to maintain accurate temperatures then great.

And sure, some methods are better, or easier than others, but I think as long as your method works for you, then keep doing you.