Can I cut the protruding conduit to the floor level and cover it with junction box?
It is allowable and you would not need to make it water-tight, however, there are neater ways to finish this job. If anything below seems too overwhelming, call an electrician.

Since you're going to cut the conduit, you'll want to locate the next junction box and pull your wires back from there before you cut. When you use a sawzall or conduit cutter, you should ream the pipe before putting on a new fitting (the wires will get in the way of this).

Here are my suggestions from easiest and least finished looking to hardest but best finished:

A) Use an LB to make a right angle at the floor level and then go flex into the cabinet.


B) If you can install a junction box in the crawl space or ceiling of the room below, do that, and run from that point to the range.

C) Use an adapter for going from metal conduit to flexible conduit, this may be buried.


If you have the ability to work under the floor, cut the conduit below the floor level, leaving yourself plenty of room for as gentle of a bend as possible. Plan a new route for your flex to come up from the floor under the cabinet and be installed in an accessible location within the cabinet. 

If necessary, replace the existing wires with wires that are able to reach your new, concealed junction box location. Considering this is for a range, make sure your wires are the proper size (likely 6 AWG).

Pull the wires through the conduit, then slip the flex and fitting over the wire. Then pull the flex into the cabinet and install into the junction box.