TO-39 transistor mounting to PCB

Mounting flush can give better heat dispersal, particularly if the PCB tracks are so designed to aid that. That said for normal low power usage I always use to mount them a little above.

You used to be able to get mounting pads (think spacers) for these and other old timer outlines.
 
My old Marantz amp has little spacers between the bottom of the transistor and the PCB. That made me wonder about spacing them above the board, maybe 0.100" or so above the board.

I'm putting together a couple Leach Amp boards that has 2N3440 and 2N5416 transistors, look like they are predrivers for the driver transistors in the circuit.
 
Looks like you're talking about a Leach amp - if you flush-mount them - it's easier to "push" the heatsinks on top ... without folding its long legs ... but there's little room for heatsinks... And they are quite warm, but think you can do without a heatsinks...i have them so i use them.
 

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