Can you provide some more specifics on what you’re trying to do? T5-HO?
If it’s T5-HO, for example a 48” fixture will take 48” 54 watt bulbs. You couldn’t possibly use 36” 39 watt without modifying the fixture to move the end caps in.
From what I’m seeing on the interwebs, undersizing the bulbs for the ballast would result in bad things. For Florescent tubes, I’m reading that the ballast is there to limit the current going to the bulb which has essentially zero resistance after being fired up and would end up oversupplying power to the bulb. Which could damage the bulb and/or ballast. (I’m picturing flames).
I can provide a link to the thread I’m reading if you’d like. Just because someone wrote it on a forum doesn’t make it right, but personally I wouldn’t try this.
It’s not as easy as putting a 20w incandescent bulb in a table lamp rated for 40w max.