I just did a similar connection arriving in Jakarta from Tokyo on a Saturday night at 2345 and connected to the Garuda flight at 0210 with time to spare. I was traveling with cary-on bags only (way way way more than 10kg, but bags fit in the overhead). There were other passengers with bags that were able to make the same connection, but that was a hussle.
Regardless of your connection, I strongly suggest applying for the evoa as you are able to use the automated customs gates which had no line. There was a long wait with many frustrated looking travelers to apply and pay for their visas at the airport. Also fill in the customs declaration ahead if you are able, if not, fill it out while you wait for bags using the kiosk and take a picture of the QR code for when you exit. Terminal 3. If you dont arrive at the same terminal the 2ish hour connection will not be possible. As others have said, the Anara hotel is clean and comfortable if you stay the night.
For your flight to Manado, I recommend sticking with Garuda. They are reliable and safe. I attempted to save over $100 on my return by booking Batik, but got the email 24 hours before that my flight had been rescheduled and I was unwilling to risk my international connection. There was no way to reach anyone for earlier rebooking options, and although there was a link to request a refund, it required WhatsApp which appears to be the only way Batik communicates. I ended up booking the Garuda flight at the last minute and all went smoothly from there. I'm now letting credit card's dispute process handle the refund from Batik.
Although I have never taken Scoot to Manado, I have had negative experiences with Scoot to/from the Philippines and they can be very strict with enforcing weight limits. They are either perfectly fine, or its a complete nightmare; there is no in between. I looked at Scoot as an option for my recent trip but the current schedule to Manado gets you there late in the afternoon, even later than previously, and connections returning to the US are very limited and may require a night in Singapore which is a great city if you have time to enjoy but not my choice for a 10 hour overnight connection between 8pm-6am.
Safe travels! I always enjoy reading trip reports. I'll be posting a report from mine very soon.