i believe linking it wouldnt affect your checkin time because its not an interlined ticket.....

one risky of buying 2 separate tickets instead of 1 with all the trips is that if your YVR - NRT is delayed and missed the connection from NRT - TPE, the both airlines (AC / NH) are not obliged to provide you any service (offer you another flight, hotel accomodation etc....)

However, they may do so as a courtesty.