When you bead a single pane window from the outside, do you bead tight to the glass or do you leave a gap and fill will putty?
timber beads?
small bead of silicone in 4 corners before glass goes in -stops water getting to joint
bed glass on thin layer of silicone.
apply even bead of silicone all round in corner where glass meets timber.
On bottom bead do second bead along bottom of glass just below where edge of bead will go.
paint ends of beads beforehand
silicone mitres
put beads in short ones first.
push beads in hard to spread mastic
bottom bead -aim for silicone to squeeze out along length of bead at join with glass -this point is vulnerable to water ingress.
What type of silicone do i use
I can putty-in window glass, but it's not a popular skill any more.
You don't. Period.
Paint does not adhere to silicone.
Use a MS polymer. They are as flexible as silicone but can be painted over. They do however cost a little more.
There are numerous options to choose from.
eg
Timbabuild
CT1
Stixall
Sikka
BTW, although they all say they can be painted over, you need to apply a waterbased primer/undercoat first otherwise any oil based paints will take weeks to dry.
As you suggested you will need to nail the wooden beadings to prevent them from bowing/warping. You can either bed them into ms polymer first or run a thin bead after. The former is probably the longer lasting option but you will benefit from having a silicone smoothing tool to hand and decorators wipes for removing "over spill".