Mark, (Portland, OR)
The toilet and the floor flange must be removed in order to drop the holding tank. Also, the termination assembly and the vent pipe must also be disconnected from the tank before it can be removed. Some flanges and toilet drains are glued, some are threaded and some use a simple friction seal with the downpipe inserted into a rubber grommet at the top of the tank. The downpipe should never extend into the holding tank more than three-quarters of an inch. Extending further into the tank is only possible with the rubber grommet even though there is a lip on the inside of the grommet. Remember, it is only rubber, so a "too long" pipe can be pushed past the lip and forced further into the tank. This may be what happened on yours. If your downpipe is threaded or cemented, it cannot extend too far into the tank because the threads and the seat of the fitting would limit its travel.
First remove the toilet and then the screws holding the flange to the floor. Try to "unscrew" the flange and downpipe together as one unit. (A simple removal tool can be made by using a short piece of 1 X 3 shelving material with two 3/8-inch holes drilled through it that match the spacing between the two existing closet bolts in the flange.
After the toilet has been removed, place the board over the closet bolts and rotate counter-clockwise). If it will not rotate it is probably cemented. If cemented, the drain pipe will have to be cut between the bottom of the floor and the top of the tank. If you have the rubber grommet or the threaded fitting into the tank, the flange and downpipe assembly will twist free and can be removed from inside the bathroom.
Careful measurements can then be made to determine if the pipe extends too far into the tank and/or if you have the needed space to install the 45-degree ells to move the inlet to a deeper section of the tank. If you have the clearance for the 45-degree fittings, then you can drop the tank, cut a new opening in the tank and have the old inlet plastic welded with a patch. Check to see if your local RV shop indeed has a plastic welding unit. Welding will be the only way to guaranty a leak-free patch.
Then reinstall the tank using the 45-degree elbows; connect the termination assembly and vent. Be sure to fill the tank with fresh water all the way up and into the toilet bowl to test the integrity of the modification.