Hi,
In general most of the substrates used should let enough heat through if you adjust the thickness right.
I say in general because there are always unexpected hiccups.
Oh and newspaper still counts as a real substrate.
If you are quick about it I don't think the substrate will have time to cool down a great deal just in the time it takes you to open the lid - if you opened it then changed the waterbowl and spotcleaned etc then yeah it will have cooled significantly.
Air temps will obviously cool much faster which could be a factor if you were using accurite probes etc but tempguns should be better. Of course if anyone knows different sing out.
dr del