Can the Second Skin armor be worn under another armor set and does the EAC, KAC and armor penalties stack?
No, bonuses of the same type do not stack
That rule is still valid for Starfinder, and while you may even convince your GM to wear two different armors, only one of them will provide you with bonuses while worn (probably the highest).
When multiple bonuses apply to the same value, different types of bonuses all apply, but in most cases bonuses of the same type do not add together (or “stack” with each other), unless a source specifies otherwise. (For an exception, see Circumstance Bonus below.) Bonuses that do not list a bonus type do stack, both with each other and with all typed bonuses. Such bonuses, often referred to as “untyped” bonuses, are among the most utilitarian of all bonuses in the game.
Armor bonuses don’t stack with other armor bonuses, but they do stack with all other bonuses to Armor Class (such as a Dexterity bonus). Armor bonuses sometimes specify that they apply only to your Energy Armor Class (EAC) or your Kinetic Armor Class (KAC). Most suits of armor provide armor bonuses to both EAC and KAC, though the specific armor bonuses a suit provides to each value often differ, as noted in the armor’s description. An armor bonus that doesn’t specify which Armor Class it applies to applies to both.
\$\begingroup\$ Wouldn't an armor giving high armor bonus to EAC stack with the one giving high armor bonus to KAC for a combined high-to-both effect, if 'That stacking rule' is the only thing preventing multiple armors? \$\endgroup\$– NoxJun 20, 2018 at 7:46
\$\begingroup\$ Most suits of armor provide armor bonuses to both EAC and KAC. So even if one armor had higher KAC than another, the bonuses are to both, not individual. \$\endgroup\$ Jun 20, 2018 at 10:50