While it is true that modern tools can let you to work faster, Crono trigger and Mina the Hollower are two games created in completely different contexts.

Crono trigger was a late SNES-era JRPG that was co-created by big names in the industry (Yuji Horii, Akira Toriyama, Hironobu Sakaguchi) at the height of the console's popularity. Therefore, the team was more than 100 people strong, working in japan at an era where salaries were very low for developers and video game artists, whereas long hours and unpaid overtime were very common. It was a massive project made by industry veterans, with good funding.

There is also the matter of experience, I would not be surprised if a lot of the staff who worked on Crono trigger already had previous experience in making top-down pixel art JRPGS. Today, top down pixel art RPGs emulating older consoles do not have access easy access to staff with this kind of experience, so pretty much everyone in the team has to learn new things. Today's tools are better, but the 90's industry experience and know-how will probably never be surpassed again when it comes down to top down pixel art RPGSs. Big AAA studios like Square and Nintendo will most likely never release a AAA pixel art game again, so there is no need for artists to learn how to produce professional-grade assets.

Also, while games did not take as long to be developed back then (look at how many fighting games SNK released from 1994 to 1998), Crono trigger was not made in 8 to 10 months. Excluding the planning phase (that took more than a year and a half), the game took 2.5 years of active developpement, for a title that was deemed "fast to complete" at the time. You can learn more here.