Fad perks, like kegs.
Open work spaces that are also quiet.
Large number of new hires.
The overuse of the word startup from large companies.
The use of the phrase drink from the firehose as if it is positive
Companies may be better set up for new employees of specific skill levels. If you are fresh out of school, then be aware that some companies will have poor onboard support.
Lack of age diversity, diversity is potentially difficult to come by, age diversity is not. This requirement may not apply to startups that cater to persons without children.
Bonus question: in general the company should pay for your travels. If you feel weird about asking and you can afford it, then drive out for the interview. Getting good interview practice is worth time and money investment. Do not feel that they owe you something because you made this decision. The company should also be willing to pay for your move to their location. This should be a requirement if you are going to accept an offer.