How does exactly armor works with an Explorator? Technically, won't the implants and mechadendrites interfere with the armor? Are they able to wear it normally? (let's say, a carapace armor or such)
Firstly, somewhat of a fluff explanation; I'll try and answer in two areas - the implants and the mechadendrites (which are technically also implants, but they're the stick-out kind):
Mechanicus implants, bar very bizarre exceptions/chaos-tainted bionics, tend to follow the human form; bionic arms/legs/eyes are typically of human size and dimensions etc. In most cases, they won't get in the way, and armour should, as a garment, particularly one so mass-produced (to supply the Imperial Guard et al), have some "give" in them (adjustable straps, space velcro etc.) to afford extra space if there is a particular chest panel that extends beyond the normal human chest dimensions.
Mechadendrites, being extensions of the Explorator, can move and twist in order to be wherever the Explorator would need them; this could extend to weaving out and through gaps in the armour; from a 40k wiki for reference, Carapace Armour
consists of large rigid plates of armaplas or ceramite molded to fit parts of the body
and it stands to reason that there wouldn't be much armour around the joints, for maneuverability. This would include around the shoulders, allowing for back-mounted 'dendrites the freedom to extend through the gaps. Failing that, an enterprising Explorator could probably make short work of some "modifications" to cut holes in the armour if you feel it wouldn't be feasible.
For other armour, like flak and mesh, they're not a rigid and difficult to pierce as Carapace, and probably get the "Doc Ock" treatment :)
An alternative viewpoint for (certainly carapace) armour is that the mechadendrites are fitted to ports on the outside of the armour, which in turn are connected to the Explorator; sort of like "bionic armour", but just for the purposes of maintaining links with the mechadrendrites; its up to the GM how they want to houserule the situation, though - I'd just say they worm through gaps in the armour.
A final viewpoint, particularly with any armour the character starts with, is that it is a custom set of armour specially designed to fit the Explorator; on a Rogue Trader, this might not be far-fetched.
Secondly, the rules explanation: the rules don't cover comfortable armour, and its typically not something people think about; there is consideration for different races (Ogryns can't use human-sized armour and vice versa, for instance) but in every case its assumed the armour fits if you're the right species...