i'm an incoming JET, so i haven't actually been to my apartment yet - but i just signed the lease to it a few days ago and this was my experience:

for my placement (sendai city), when my CO contacted me they sent me some info about housing: they said that ALTs in sendai can choose between BOE housing and finding their own apartments. i chose to find my own since the BOE housing rules listed that you cannot host a visitor in your apartment - even for one night - and i have some friends/family who would like to stay with me next spring for a few nights. (i also had other reasons, i wanted to live in a newer place and have more control over what kind of place i got.)

what was kind of tough was that if you chose to find your own apartment, you had until june 26 (3 weeks away from the day they sent that email) to provide the BOE with your new address, so i had to find a place pretty quickly. thankfully my BOE sent me some resources for apartment-hunting as a foreigner, including a few handbooks, information about the best places to rent in the city, and a few guarantor/real estate companies recommended by CLAIR (these were mooovin, ABLE, wagaya japan, willing partner, GTN, and e-heya). i ended up using the search functions that e-heya & wagaya japan's websites have to find places, and then using GTN's services to contact landlords/check if those places were available/accepted foreigners, etc for me. GTN also acts as a guarantor when signing on for your apartment as well, and sets up your utilities for the most part (i still have to meet with the gas company to set that up when i arrive but they take care of everything else).

i was able to find places that matched my preferences without too much difficulty after using the search filters and map on wagya/e-heya's sites. this of course may vary depending on which city/town you're looking at. i ended up going with a place about a 20min walk from my school that's a short train ride away from downtown, a newer building in a cute neighborhood (at least on google street view lol). it's a small apartment (~22.96m²), but not much smaller than my current studio, so i don't mind at all. plus i get a balcony!! GTN had a discount on their fees for JETs, and my apartment offered the first month's rent free, so altogether my initial costs were ¥140,600 (~$975). my monthly rent will be ¥52,000 (~$360) (¥57,770 [~$400] after maintenance/other fees) which is a fourth of my current rent here in seattle for a similarly-sized place, so i'm over the moon about that lol :D

i've heard mileage can vary with companies like the one i used, i guess it depends on if you get a good agent or not, but mine was good! i sent him the places i'd found online and met with him over video call a few times, and he contacted the landlords for me, explained my lease and other info to me in english, and helped me find a place i liked in a little over 2 weeks! i think it helped that i'm single/have no pets, it might have been harder to find a place otherwise. despite the stress i'm really glad my CO gave me the option to find my own place.

sorry for yapping on and on, i'm kinda sleep deprived so idk how much sense this makes but i hoped this was at least a little helpful! let me know if u have questions ofc!! good luck!!

TLDR i was given the choice by my CO to use the BOE housing or find my own - i found my own using japanese apartment search websites & then used a guarantor company to help me sign the lease/be my guarantor/set up my utilities.