I've used several different types of shuttles with no problem. Though, shuttles like other ships can not collide with other ships in SFC3. They will be destroyed if they collide with a planet, starbase, or mine.
My txt files:
-20 SH 1 0 5 3000 300 2000 4000 41 Fed-Shuttle fft PrimaryHP:1:330_30:2:330_30 HeavyHP:12:330_30 HullHP:1:2:3 BridgeHP:1:2 ship Mines:0:0:0 Marines:0:0:0 Shuttles:0:0:0
Federation Fed-Shuttle Federation Shuttle fft F-TRACTOR-I:3 F-TRANSPORTER-I:1 F-COMPUTER-I:1 PHASER IXS:1 OFFICER:ENGINEER:SWARTLEY:13:12:11:Junior:3. Skilled:3. Skilled:3. Skilled:3. Skilled:3. Skilled:3. Skilled:3. Skilled:3. Skilled:3. Skilled:5. Expert:5. Expert:5. Expert:3. Skilled:3. Skilled:3. Skilled:3. Skilled:3. Skilled:3. Skilled: OFFICER:SECURITY:LEDERMAN:11:13:14:Junior:3. Skilled:3. Skilled:3. Skilled:3. Skilled:3. Skilled:3. Skilled:3. Skilled:3. Skilled:3. Skilled:3. Skilled:3. Skilled:3. Skilled:5. Expert:5. Expert:5. Expert:3. Skilled:3. Skilled:3. Skilled: OFFICER:HELM:HARTNELL:10:14:10:Junior:5. Expert:5. Expert:5. Expert:3. Skilled:3. Skilled:3. Skilled:3. Skilled:3. Skilled:3. Skilled:3. Skilled:3. Skilled:3. Skilled:3. Skilled:3. Skilled:3. Skilled:3. Skilled:3. Skilled:3. Skilled: OFFICER:OPS:YA-JUE:12:14:11:Junior:3. Skilled:3. Skilled:3. Skilled:5. Expert:5. Expert:5. Expert:3. Skilled:3. Skilled:3. Skilled:3. Skilled:3. Skilled:3. Skilled:3. Skilled:3. Skilled:3. Skilled:3. Skilled:3. Skilled:3. Skilled: OFFICER:TACTICAL:KOSNETT:11:11:11:Junior:3. Skilled:3. Skilled:3. Skilled:3. Skilled:3. Skilled:3. Skilled:3. Skilled:3. Skilled:3. Skilled:3. Skilled:3. Skilled:3. Skilled:3. Skilled:3. Skilled:3. Skilled:5. Expert:5. Expert:5. Expert: OFFICER:MEDICAL:BRATTAIN:14:10:14:Junior:3. Skilled:3. Skilled:3. Skilled:3. Skilled:3. Skilled:3. Skilled:5. Expert:5. Expert:5. Expert:3. Skilled:3. Skilled:3. Skilled:3. Skilled:3. Skilled:3. Skilled:3. Skilled:3. Skilled:3. Skilled: F-ARMOR-I:2 F-SHIELD-I:1 F-SHIELD-I:2 F-SHIELD-I:4 F-SHIELD-I:3 PHASER IXS:2 PHOTON TORPEDO:12 F-IMPULSE-II:2 F-WARP-I:1 F-THRUSTER-III:3