I've done some more testing on apartments this morning.
I moved a sim into empty apartment 17 Culpepper House, Spice District with weekly rent $400, deposit $800 and furnishings $8,095 Lot Value was less than furnishings ($8,008). Left with $11,105 so you only pay deposit and furnishings to move in.
Then i motherloded to see a middle-valued apartment (starting funds $61,105) and moved to 920 Medina, Art District with weekly rent $1K, deposit $800 and furnishings $29,380. Firstly if i keep furniture then the money was $31,725 so the only thing charged was $29,380 (in effect you get your deposit back and then it goes into this new rental, much like real life). Lot value again was less than furnishings ($26,927).
I motherloded twice more ($131,725), keeping furniture, moved to 1010 Alto Apartments, Uptown with weekly rent $3500, deposit $15,500 and furnishings $100,215.
Again i got charged for deposit -$800 paid from last place and furniture only. Again Lot Value was less than furniture ($90, 360).
Therefore i think only "furniture" value should be considered in Apartments.
As an aside, i notice lot value goes down for apartments regardless of keeping/selling furniture which would make verifying "score" difficult, whereas if you "sell furniture" at move screen on a house, the house you have moved out of has a value the same as the Lot Value score so is easier to verify.
Maybe go back to no Apartments? Sorry folks, i think Apartments was added after i queried it yesterday. It seemed okay at the time but depends what the team thinks about the new information surrounding verification which i wasn't aware of until deep diving today.