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For example could a squad of 9 shock troopers and an enginseer embark on a chimera for whatever reason even though they are from separate squads?

If they are from seperate units, No. Only super heavy transports allow that.

And SM Combat Squads.

But as a general rule: no, only one unit at a time.

also don't forget that Independant Characters can join a unit and board the same transport. Is the Engseer an IC?

Short answer: No. Other than Super heavy, only 1 unit at a time.

Longer answer:

Independent Characters are allowed to join with other units "for all rules purposes". When an IC joins another unit they become one unit and therefore satisfy the rule of only 1 unit at a time in a transport.

The only real wrinkle is a 10 man marine unit. Marines can combat squad and the full squad can be embarked in a transport even if they split up.

So, if your enginseer is an IC that can join your shock troops then yes they can both enter the chimera.