Monster Examples:
Dead Suns 1-pg58 CR5 Garaggakal:
Skills:
-Acrobatics +16 (5Rank+5Dex+3class?=13?)
-Athletics +11 (5Rank+2Str+3class?=10?)
-Stealth +16 (5Rank+5Dex+3class?=13?)
-Survival +11 (5Rank+2Wis+3class?=10?)
Dead Suns 1-pg58 CR6 Rauzhant:
Skills:
-Acrobatics +18 (6Rank+2Dex+3class?=11?)
-Intimidate +13 (6Rank+0Cha+3class?=9?)
-Survival +13 (6Rank+0Wis+3class?=9?)
First Encounter-pg14 CR5 Sarcesian:
Skills:
-Acrobatics +17 (5Rank+5Dex+3class?=13?)
-Bluff +12 (5Rank+2Cha+3class?=10?)
-Computers +12 (5Rank+3Int+3class?=11?)
-Survival +12 (5Rank+0Wis+3class?=8?)
*Note they have Racial Traits instructions and include 0 skill bonuses
In fact the only monster examples that ever had any skills without invisible bonuses seem to be monsters CR1 and lower.
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There isn't much about NPCs in the Core Book:
pg389 says they should have similar skill to party
However
pg326 under "Crew Level" says 1 crew member will be Master at any given ship skill giving them Tier(CR)*1.5+9 (If I am reading "1-1/2 * the NPC's ranks" correctly). So at CR1 the opposing pilot has +10 pilot and at CR20 would have +39. Both numbers I don't think any player can possibly reach at the same level, much less a character not designed "just to be the pilot".
Only other info I can find is pg392 under "Skill DC's" says a challenging skill DC should be 15+1-1/2*CR or APL. When a character only gains 1rank a level how would a character keep up with that progression? A challenging CR20 skill check would be DC45. A Lv20 Player could have max20ranks +max9Stat(18start+6enhancment+4level), for a total bonus of +29...
There are a couple small bonuses from feats, race, or class but that means a character is required to max a single stat and ranks in the connected skill and look for other bonuses just to have a chance of keeping up with this games scaling difficulties. If you are not built focused on a given task you will fail at higher levels.
Oh and lastly starship actions have a 2*Tier scaling meaning the numbers get impossible even faster. Or you stop upgrading your ship so it's Tier stays low and the party can actually do combat actions...
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tldr: I think the designers expected more +skill magic items like pathfinder, but they removed most of them. They designed the monsters with and DC's with this in mind and it makes mid-high level play impossible due to faster scaling than level.