If you haven't already worked through them, then you might benefit from my tutorials on diatonic modes.

Modes of the Major Scale
http://www.guitartricks.com/tutorial/370/ 

Practicing Major Modes  
http://www.guitartricks.com/tutorial/770/

Practicing Minor Modes
http://www.guitartricks.com/tutorial/2630/

In general, there are 2 ways of looking at modes:

Structural

Each mode relates to a parent scale. So you are always in one major scale, G major for example, and the various modes are just ways of playing a G major scale, but starting on each note in turn. Often this is used to stay in one key, but play over the chord changes within the key.  This is origin of the modern diatonic modes:  they are the major diatonic scale but sequenced from a different reference point.

Ornamental

You just play whichever mode you like the sound of at the time without regard to a specific key signature. This requires that you know & apply the scale or mode interval formula.  Each mode has an interval formula that implies it's own harmony.

What you are suggesting is more of the latter, ornamental.  Especially when you mention altering a mode by changing a scale degree/interval.  Because this is the fundamental difference between the modes: the scale degrees, or interval formula.  That's exactly what gives each mode it's unique, characteristic sound.

Some musical contexts have an incomplete harmonic information.  For example, you have a bass player riding a G note.  What mode do you use?  Your choices are wide open at this point, any mode starting on G simply based on what sound you want to create.  You could even switch between modes from line to line or within a line.

The bass player adds a B & D, now there is a major triad implying a G major chord as your musical context.  What mode do you use?  Any one of the major modes will sound musically appropriate, ionian, lydian, mixolydian.  You can even switch between them on lines as you go.  Mix & match!

The bass player starts walking the complete G major scale.  Now you have the musical context defining ionian, the major scale.  You could play any major mode, but you should be aware that the minor 7th of mixolydian might clash with the major 7th of ionian should they occur together rhythmically, or even suggest dissonance in the same temporal vicinity.

The point here is that knowing the intervals of the modes is just a starting point.  Practicing them to internalize the sound is the next step.  Then you're ready to apply it in a musical context, which is often dynamic & requires forethought, planning & creativity.

Hope that helps!