Yes it can be a problem trying to cram in all the extra stuff, especially with some airplanes that have smaller fuselages.
They do have a special BEC device that can use a single battery pack to power both the ignition system and RC system. it uses RFI filters and adjustable voltage regulators. Here is one such device http://www.tech-aero.net/ultra-ibec

The NGH engines use a RCexl ignition system. The RCexl ignition unit has a maximum voltage input of 6.0v. They really mean it too. You cannot use a 5 cell nicad or NMH pack with it, as a fully charged 5 cell pack exceeds 6.0v. The ignition unit will burn out if the voltage exceeds 6.0v. I use a four cell 4.8v battery pack for the ignition system, which when fully charged outputs a little over 5v too. But it stays under the 6.0v limit. So if you just have to use a Lipo or LiFe battery pack or something like that then you will need to use a voltage regulator to supply 5.0v to the ignition module. The RCexl ignition systems are designed for 4.8v battery packs, so they have their best performance at that voltage level anyway. Trying to power them with higher voltages does not make them work any better.