Aligning Control in Manipulate

You can use the Method suboption "ControlAreaDisplayFunction" to modify the control labels to have the same size:

Manipulate[a, 
 Control[{a, 0, 1, 0.1}], 
 Dynamic[If[a < 1, Control[{{abc, 0}, {0, 1}}], 
   Control[{{abcdef, 0}, {0, 1}}]]], ControlPlacement -> Left, 
 ContentSize -> {100, 100}, Alignment -> Center, 
 Method -> {"ControlAreaDisplayFunction" -> 
   (Replace[#, RawBoxes[s_] :> Item[s, ItemSize -> {5, 2}], All] &)}]

Alternatively, you can use

Method -> {"ControlAreaDisplayFunction" -> (Replace[#, 
      RawBoxes[s_] :> Pane[s, Alignment -> Right, 
        ImageSize -> Rasterize["abcdef", "RasterSize"]], All] &)}

Note: As far as I know the option Method and its suboptions are not documented. I came across $ManipulateMethodOptions during a spelunking expedition using ??*`*Manipulat*. Clicking on one of the results gave:

Manipulate`Dump`$ManipulateMethodOptions
{"BookmarkAnimationClipping" -> True, 
 "BookmarkDurationMultiplier" -> 1.5`, 
 "ContentAreaBackground" -> Automatic, 
 "ControlAreaDisplayFunction" -> (#1 &), "ExtraVariables" :> {}, 
 "DynamicCore" -> True, "HeuristicControllerBindings" -> True, 
 "InlineCell" -> False, "SingleEvaluation" -> True, 
 "ShowControls" -> True, "TemplateExpand" -> False}

Update: An alternative approach is to wrap control labels with Pane and use the rastersize of the longest label as the ImageSize:

is = Rasterize["abcdef", "RasterSize"];
pane = Pane[#, ImageSize -> is, Alignment -> Right] &;

Manipulate[a, 
 Control[{{a, 0, pane@"a"}, 0, 1, 0.1}], 
 Dynamic[If[a < 1, Control[{{abc, 0, pane@"abc"}, {0, 1}}], 
   Control[{{abcdef, 0, pane@"abcdef"}, {0, 1}}]]], 
 ControlPlacement -> Left, ContentSize -> {100, 100}, Alignment -> Center]

Update 2: To make a control invisible without adding vertical space between its neighbors:

Manipulate[a, 
 Dynamic @ Grid[{{pane @ "a", Control[{{a, 0, ""}, 0, 1, 0.1}]}, 
    If[a < 1, {pane @ "abcdef", Control[{{abcdef, 0, ""}, {0, 1}}]}, ## &[]], 
   {pane@"b", Control[{{b, 0, ""}, 0, 1, 0.1}]}}, 
    Alignment -> {{Right, Left}, Automatic}], ControlPlacement -> Left]

You can put your Controls in a Column to lay out your controls in a arbitrary way. From here, you can use the Alignment option for Column.

Manipulate[a, 
 Column[{Control[{{a, 0}, {0, 1}}], 
   Dynamic[If[a == 0, Control[{{abc, 0}, {0, 1}}], 
     Control[{{abcdef, 0}, {0, 1}}]]]}, Alignment -> Right], 
 ControlPlacement -> Left]

You could use Grid. Like so:

Manipulate[a,
  Dynamic @
    Grid[
      {{"a", Control[{{a, 0, ""}, 0, 1, 0.1}]},
       If[a < 1,
         {"abc", Control[{{abc, 0, ""}, {0, 1}}]}, 
         {"abcde", Control[{{abcdef, 0, ""}, {0, 1}}]}]},
       Alignment -> {{Right, Left}, Automatic}],
  ControlPlacement -> Left]

Update

The following is added to address concerns raised by the OP in a comment to this answer.

Maybe this will work for you.

Manipulate[a,
  Dynamic @
  Grid[
    {{"a", Control[{{a, 0, ""}, 0, 1, 0.1}]},
     If[a < 1,
       {"abc", Control[{{abc, 0, ""}, {0, 1}}]},
       {"", SpanFromLeft}]},
     Alignment -> {{Right, Left}, Automatic}],
  ControlPlacement -> Left]