I'm a
BA player so your
DA mileage may vary.
But our Sanguinary Novitiates (command squad apothecaries) start with a bolt pistol, chainsword and narthecium. However they have no access to upgrades ( :( )
I conclude this because in the squad loadout it says...
Power armour
Bolt pistol
Chainsword (Veterans and Sanguinary Novitiate only)
Frag grenades
Krak grenades
Narthecium (Sanguinary Novitiate only)
Power sword and combat shield (Company Champion only)
So that means every model has power armour, bolt pistol and frag&krak grenades, as nowhere does it specify only a few models.
And the Sanguinary Novitiate additionally has a chainsword and narthecium.
The Sanguinary Novitiate cannot take any upgrades [apart from a jump pack, which is a squad wide upgrade] since all upgrades specify a 'Veteran' of whom the Sanguinary Novitiate is not legally speaking (he's a Sanguinary Novitiate).
Which means he cannot replace his bolt pistol or his chainsword with anything, he's stuck the way he is.
Hopefully that helps you understand the way it works and you can apply that to your own codex